Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Rapid methods of measuring the effects of an agent in a biological or chemical assay. The assay usually involves some form of automation or a way to conduct multiple assays at the same time using sample arrays.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The functional hereditary units of BACTERIA.
The relationships of groups of organisms as reflected by their genetic makeup.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Genotypic differences observed among individuals in a population.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Any method used for determining the location of and relative distances between genes on a chromosome.
Proteins found in any species of bacterium.
Sequential operating programs and data which instruct the functioning of a digital computer.
Preclinical testing of drugs in experimental animals or in vitro for their biological and toxic effects and potential clinical applications.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Biochemical identification of mutational changes in a nucleotide sequence.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)
Deoxyribonucleic acid that makes up the genetic material of viruses.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Ribonucleic acid that makes up the genetic material of viruses.
Large collections of small molecules (molecular weight about 600 or less), of similar or diverse nature which are used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, or other chemical interactions.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
Established cell cultures that have the potential to propagate indefinitely.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
A genus of HALOBACTERIACEAE distinguished from other genera in the family by the presence of specific derivatives of TGD-2 polar lipids. Haloarcula are found in neutral saline environments such as salt lakes, marine salterns, and saline soils.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Methods utilizing the principles of MICROFLUIDICS for sample handling, reagent mixing, and separation and detection of specific components in fluids.
Controlled operations of analytic or diagnostic processes, or systems by mechanical or electronic devices.
The functional hereditary units of VIRUSES.
The design or construction of objects greatly reduced in scale.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The process of finding chemicals for potential therapeutic use.
Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
A technology, in which sets of reactions for solution or solid-phase synthesis, is used to create molecular libraries for analysis of compounds on a large scale.
Proteins prepared by recombinant DNA technology.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The study of fluid channels and chambers of tiny dimensions of tens to hundreds of micrometers and volumes of nanoliters or picoliters. This is of interest in biological MICROCIRCULATION and used in MICROCHEMISTRY and INVESTIGATIVE TECHNIQUES.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Databases devoted to knowledge about specific genes and gene products.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The deliberate and methodical practice of finding new applications for existing drugs.
The rate dynamics in chemical or physical systems.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The protein complement of an organism coded for by its genome.
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
Proteins found in any species of virus.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.
A method of detecting gene mutation by mixing PCR-amplified mutant and wild-type DNA followed by denaturation and reannealing. The resultant products are resolved by gel electrophoresis, with single base substitutions detectable under optimal electrophoretic conditions and gel formulations. Large base pair mismatches may also be analyzed by using electron microscopy to visualize heteroduplex regions.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
A mass spectrometric technique that is used for the analysis of large biomolecules. Analyte molecules are embedded in an excess matrix of small organic molecules that show a high resonant absorption at the laser wavelength used. The matrix absorbs the laser energy, thus inducing a soft disintegration of the sample-matrix mixture into free (gas phase) matrix and analyte molecules and molecular ions. In general, only molecular ions of the analyte molecules are produced, and almost no fragmentation occurs. This makes the method well suited for molecular weight determinations and mixture analysis.
Proteins obtained from ESCHERICHIA COLI.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
The portion of an interactive computer program that issues messages to and receives commands from a user.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.
The sum of the weight of all the atoms in a molecule.
A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of PROTEINS; NUCLEIC ACIDS; and CARBOHYDRATES. (Segen, Dictionary of Modern Medicine, 1992)
A method of measuring the effects of a biologically active substance using an intermediate in vivo or in vitro tissue or cell model under controlled conditions. It includes virulence studies in animal fetuses in utero, mouse convulsion bioassay of insulin, quantitation of tumor-initiator systems in mouse skin, calculation of potentiating effects of a hormonal factor in an isolated strip of contracting stomach muscle, etc.
A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS.
Microdevices that combine microfluidics technology with electrical and/or mechanical functions for analyzing very small fluid volumes. They consist of microchannels etched into substrates made of silicon, glass, or polymer using processes similar to photolithography. The test fluids in the channels can then interact with different elements such as electrodes, photodetectors, chemical sensors, pumps, and valves.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Software designed to store, manipulate, manage, and control data for specific uses.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Use of various chemical separation and extraction methods, such as SOLID PHASE EXTRACTION; CHROMATOGRAPHY; and SUPERCRITICAL FLUID EXTRACTION; to prepare samples for analytical measurement of components.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The genetic complement of a BACTERIA as represented in its DNA.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
INFLAMMATION of any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Causes of gastroenteritis are many including genetic, infection, HYPERSENSITIVITY, drug effects, and CANCER.
An actinomycete from which the antibiotics STREPTOMYCIN, grisein, and CANDICIDIN are obtained.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
Small uniformly-sized spherical particles, of micrometer dimensions, frequently labeled with radioisotopes or various reagents acting as tags or markers.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
An individual having different alleles at one or more loci regarding a specific character.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.
Substances that reduce the growth or reproduction of BACTERIA.
Enzymes found in many bacteria which catalyze the hydrolysis of the amide bond in the beta-lactam ring. Well known antibiotics destroyed by these enzymes are penicillins and cephalosporins.
Description of pattern of recurrent functions or procedures frequently found in organizational processes, such as notification, decision, and action.
Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses).
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Condensation products of aromatic amines and aldehydes forming azomethines substituted on the N atom, containing the general formula R-N:CHR. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
An array of tests used to determine the toxicity of a substance to living systems. These include tests on clinical drugs, foods, and environmental pollutants.
Substances that comprise all matter. Each element is made up of atoms that are identical in number of electrons and protons and in nuclear charge, but may differ in mass or number of neutrons.
The genomic analysis of assemblages of organisms.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
Chromatographic techniques in which the mobile phase is a liquid.
The functional hereditary units of FUNGI.
Elements of limited time intervals, contributing to particular results or situations.
Methods used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Organized activities related to the storage, location, search, and retrieval of information.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Deoxyribonucleic acid that makes up the genetic material of plants.
Halogenated anti-infective agent that is used against trematode and cestode infestations.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The concentration of a compound needed to reduce population growth of organisms, including eukaryotic cells, by 50% in vitro. Though often expressed to denote in vitro antibacterial activity, it is also used as a benchmark for cytotoxicity to eukaryotic cells in culture.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Methods of creating machines and devices.
DNA present in neoplastic tissue.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Transmission of information over distances via electronic means.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Transport proteins that carry specific substances in the blood or across cell membranes.
The functional hereditary units of PLANTS.

Accurate taxonomic assignment of short pyrosequencing reads. (1/2909)

Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.  (+info)

Identification and classification of small RNAs in transcriptome sequence data. (2/2909)

Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.  (+info)

Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa. (3/2909)

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AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay. (4/2909)

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Introduction into the analysis of high-throughput-sequencing based epigenome data. (5/2909)

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The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. (6/2909)

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Next-generation genomics: an integrative approach. (7/2909)

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. (8/2909)

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Publisher: University of Delaware. Date Issued: 2015. Abstract: Viral infection and lysis are important processes contributing to the diversification and evolution of microbial communities. In marine ecosystems that cover 70% of the earths surface, there are ~10 million viruses per milliliter of seawater, indicating an incredible diversity of viruses waiting to be explored. An important breakthrough in viral ecology was the application of high-throughput DNA sequencing to entire viral communities. Known as shotgun viral metagenomics, this approach allows access to the majority of viruses that cannot be maintained in culture. Viral metagenomics has revealed surprising insight into ancient associations between viruses and hosts. However, making quantitative inferences from next generation sequencing data requires careful evaluation of viral isolation and DNA library preparation techniques. Many library preparation strategies employ some form of amplification to obtain sufficient DNA for ...
Background Recent high throughput sequencing technology can handle generating plenty of data for bacterial genome sequencing tasks. be utilized to compute a design graph that presents the most appealing contig adjacencies to be able to help biologists in completing the entire genomic series. The design graph shows exclusive contig orderings where feasible and the very best alternatives where required. Conclusions Our brand-new algorithm for contig buying uses series similarity aswell as phylogenetic details to estimation adjacencies of contigs. An assessment of our execution implies that it performs much better than latest approaches while getting much faster at the same time. Today the nucleotide sequences of several genomes are known Background. In the initial genome tasks the procedure of acquiring the DNA series by multi-step clone-by-clone sequencing strategies was pricey and Kenpaullone tedious. Currently the most frequent strategy for de-novo genome sequencing is normally = (data files. ...
Cyanobacteria-dominated blooms in Upper Klamath Lake, Oregon, create poor water quality and produce microcystins that may be detrimental to local wildlife and human health. Genetic tools, including high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR), have been shown to improve the identification and quantification of key groups associated with these blooms over more traditional techniques. We examined the seasonal and interannual variations in nutrient (nitrogen and phosphorus) concentrations between 2013 and 2014 to describe the relations between these factors and the growth dynamics of Aphanizomenon and toxigenic Microcystis as described by DNA sequencing and qPCR. Although total nutrients and chlorophyll a concentrations were similar between years, qPCR results showed the cyanobacterial populations to be 40 times larger in 2014 and indicated a large shift from an Aphanizomenon-dominant, low microcystin-level regime in 2013 to one dominated later in the season by
TY - GEN. T1 - Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. AU - Oesper, Layla. AU - Mahmoody, Ahmad. AU - Raphael, Benjamin J.. PY - 2013/4/3. Y1 - 2013/4/3. N2 - Cancer is a disease driven in part by somatic mutations that accumulate during the lifetime of an individual. The clonal theory [1] posits that the cancerous cells in a tumor are descended from a single founder cell and that descendants of this cell acquired multiple mutations beneficial for tumor growth through rounds of selection and clonal expansion. A tumor is thus a heterogeneous population of cells, with different subpopulations of cells containing both clonal mutations from the founder cell or early rounds of clonal expansion, and subclonal mutations that occurred after the most recent clonal expansion. Most cancer sequencing projects sequence a mixture of cells from a tumor sample including admixture by normal (non-cancerous) cells and different subpopulations of cancerous cells. In addition ...
...Next-generation DNA sequencing (NGS) technology has revolutionized bio......,Essential,informatics,methods,and,tools,for,analyzing,the,explosion,of,NGS,data,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Next-generation DNA sequencing of image-guided biopsy samples collected by multiple sites reveal predictive biomarkers for cancer treatment.
RNA-Sequencing (RNA-Seq) broadly refers to a family of experimental techniques that give researchers the ability to study the transcriptional landscapes of cells and tissues quantitatively by exploiting high throughput sequencing technology. Currently, the most commonly used sequencing platforms are provided by Illumina, which uses a fluorescence-based paradigm for reading the bases in a nucleotide sequence. One alternative option is provided by Ion Torrent, which is built around the use of pH measurements to read nucleotide sequences. In addition to the distinct sequencing technologies used by these two platforms, there are smaller differences in the types of data they generate. In Illumina data all sequence reads generated during a single experiment have the same lengths, while the lengths of Ion Torrent reads vary. Additionally, the current generation of Illumina instruments can generate sequence reads from both ends of a fragment (paired-end reads), while Ion Torrent cannot.. Prior studies ...
Abstract:. This presentation aims to provide an overview of why we need next generation sequencing platforms and how the different next generation sequencing platforms perform. Moreover, some data on implementation and outcome of the Dutch experience within the Center for Personalized Cancer Treatment will be discussed. One of the challenges of increased targeted treatment for cancer is to select our patients. Novel targeted therapies require an ever-increasing number of predictive biomarker determinations on the limited amount of tissue of patients with metastatic disease. This increasing demand for predictive biomarkers presents us with challenges in the realm of tissue availability, cost-effective use of diagnostics and limiting the time-to-proper diagnosis. Part of this challenge can be resolved by introducing the use of next generation sequencing techniques to multiplex genetic diagnostics. We show that we can validate and implement the Ion Torrent based technology for diagnostic ...
The availability and throughput of next generation sequencing technologies has enabled the rapid and efficient sequencing of transcriptomes for model and non-model species. The majority of de novo transcriptome assemblies in non-model organisms have in the past been produced using the long reads (300-600 bp) generated using Roche 454 [24]. With the recent developments in sequencing technology, short read sequencers (90-400 bp), such as Illumina and Ion Torrent, are starting to be more commonly used for the generation of large next generation sequencing data sets, as the costs are much lower for the same output [25]. Consequently, the use of short read sequencers to generate de novo transcriptome assemblies for non-model organisms may lead to a more complete gene set for these species at a lower cost. The reliability of de novo transcriptome assemblies generated from short read sequencers, however, needs to be validated to ensure that assemblies are accurate and wont compromise the downstream ...
Unlock the full value of your next-generation sequencing (NGS) data sets from Illumina HiSeq/MiSeq/NextSeq/HiSeq X Ten, Roche 454 GS-FLX, LifeTechnologies Solid and Iontorrent /IonProton PGM, and PacBio platforms.. Bespoke NGS data analysis: QFAB provides tailored bioinformatics services to biologists across the spectrum of computational techniques and services applicable to molecular biology and next generation sequencing. QFAB researchers design and implement custom bioinformatics approaches that are developed in consultation with researchers for specific questions in molecular biology.. We can also integrate your genomics data with other -omics, microarrays and clinical datasets.. Our NGS data analysis services include:. Whole genome sequencing data analysis. ...
Next Generation Sequencing Market - (Technology Type - Whole Genome Sequencing, Targeted Resequencing, RNA Sequencing, Whole Exome Sequencing, and De Novo Sequencing); (Application - Oncology, Genetic Screening, Infectious Diseases, Drug and Biomarker Discovery, Agriculture & Animal Research, Idiopathic Diseases and others): Market Growth, Future Prospects and Competitive Analysis, 2017-2025 the market was valued at USD 3.7 Bn in 2017, and is expected to reach USD 20.6 Bn by 2025, expanding at a CAGR of 21.5% from 2017 to 2025.. Browse Full Report Click Here: http://www.acutemarketreports.com/report/next-generation-sequencing-market. Market Insights. Next generation sequencing is a high-throughput sequencing that enables sequencing and assembling of number of short DNA reads at a small period of time and with a better accuracy. The introduction of next generation sequencing technologies has ensured massive changes in the sequencing process by providing better output, higher speed, flexibility ...
DNA nanoball sequencing is a high throughput sequencing technology that is used to determine the entire genomic sequence of an organism. The method uses rolling circle replication to amplify small fragments of genomic DNA into DNA nanoballs. Fluorescent probes bind to complementary DNA and the probes are then ligated to anchor sequences bound to known sequences on the DNA template. The base order is determined via the fluorescence of the ligated and bound probes. This DNA sequencing method allows large numbers of DNA nanoballs to be sequenced per run at lower reagent costs compared to other next generation sequencing platforms. However, a limitation of this method is that it generates only short sequences of DNA, which presents challenges to mapping its reads to a reference genome. The company Complete Genomics uses DNA nanoball sequencing to sequence samples submitted by researchers. DNA Nanoball Sequencing involves isolating DNA that is to be sequenced, shearing it into small 400 - 500 base ...
Applied Maths NV today announces that it has released a new version of its flagship software suite BioNumerics that allows de novo assembly to be performed on next generation sequencing data. This new feature, available in version 6.6, consolidates the development of BioNumerics into a complete and fully integrated suite for preprocessing and analysis of NGS data.
Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU
TY - JOUR. T1 - Genome Detective:. T2 - an automated system for virus identification from high-throughput sequencing data. AU - Michael, Vilsker, AU - Yumna, Moosa,. AU - Sam, Nooij, AU - Vagner S., Fonseca, AU - Yoika, Ghysens, AU - Korneel, Dumon,. AU - Raf, Pauwels, AU - Luiz Carlos, Júnior Alcântara,. AU - Vanden Eynden, Ewout. AU - Vandamme, AM. AU - Deforche, Koen. AU - de Oliveira, Túlio. PY - 2019/3/1. Y1 - 2019/3/1. N2 - Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the ...
Roche and Precision System Science, Co., Ltd (PSS) have announced the signing of an exclusive agreement to develop and manufacture a fully automated emulsion PCR instrument for Roches portfolio of next-generation sequencing platforms. It is intended to support Roches GS Junior and GS FLX+ systems as well as the sequencing platforms that Roche is currently developing.
Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribute genetic change(s) at a single locus to a specific phenotype. In common diseases, where multiple genetic variants within and across genes contribute to disease, binary modelling cannot capture the burden of pathogenicity harboured by an individual across a given gene/pathway. We present GenePy, a novel gene-level scoring system for integration and analysis of next-generation sequencing data on a per-individual basis that transforms NGS data interpretation from variant-level to gene-level. This simple and flexible scoring system is intuitive and amenable to integration for machine learning, network and topological approaches, facilitating the investigation of complex phenotypes. Whole-exome sequencing data from 508 individuals were used to generate GenePy scores. For each variant a score is
Mapping reads to a reference sequence is a common step when analyzing allele effects in high-throughput sequencing data. The choice of reference is critical because its effect on quantitative sequence analysis is non-negligible. Recent studies suggest aligning to a single standard reference sequence, as is common practice, can lead to an underlying bias depending on the genetic distances of the target sequences from the reference. To avoid this bias, researchers have resorted to using modified reference sequences. Even with this improvement, various limitations and problems remain unsolved, which include reduced mapping ratios, shifts in read mappings and the selection of which variants to include to remove biases. To address these issues, we propose a novel and generic multi-alignment pipeline. Our pipeline integrates the genomic variations from known or suspected founders into separate reference sequences and performs alignments to each one. By mapping reads to multiple reference sequences and ...
Author(s): Yang, Yi-Wen | Advisor(s): Jiang, Tao | Abstract: Next-generation sequencing (NGS) technologies are able to sequence DNA or RNA molecules at unprecedented speed and with high accuracy. Recently, NGS technologies have been applied in a variety of contexts, e.g., whole genome sequencing, transcript expression profiling, chromatin immunoprecipitation sequencing, and small RNA sequencing, to accelerate genomic researches. The size of NGS data is usually gigantic such that the data analysis in these applications of NGS largely relies on efficient computational methods. Due to the critical demand for high performance computational algorithms, in the past few years, my research interest was focused on designing novel algorithms to address challenges in NGS data analysis. The main theme of this dissertation includes algorithmic solutions to three crucial problems in NGS data analysis, two arising from differential expression analysis using high-throughput mRNA sequencing (RNA-Seq) and the other from
DNA sequencing is a method to decipher the base sequence in nucleic acids. The elucidation of the DNA sequence is essential for the understanding of virtually all biological processes e.g. human disease biology, inheritance, immunology, oncology, cellular biology. First generation sequencing devices use the capillary electrophoresis-based Sanger sequencing technique. The invention of the Next Generation Sequencing (NGS) technique massively improved the weaknesses of the 1st generation sequencing technique e.g. low throughput, scalability, speed, and resolution. NGS allows massive parallel sequencing which reduces the costs and increases the speed of DNA sequencing. Automated NGS prep ...
DNA sequencing is a method to decipher the base sequence in nucleic acids. The elucidation of the DNA sequence is essential for the understanding of virtually all biological processes e.g. human disease biology, inheritance, immunology, oncology, cellular biology. First generation sequencing devices use the capillary electrophoresis-based Sanger sequencing technique. The invention of the Next Generation Sequencing (NGS) technique massively improved the weaknesses of the 1st generation sequencing technique e.g. low throughput, scalability, speed, and resolution. NGS allows massive parallel sequencing which reduces the costs and increases the speed of DNA sequencing. Automated NGS prep ...
Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel therapeutic strategies against parasitic infections. However, none of transcriptomic studies have extensively covered ES protein prediction for identifying novel therapeutic targets, especially as parasites adopt non-classical secretion pathways. We developed a semi-automated computational approach for prediction and annotation of ES proteins using transcriptomic data from next generation sequencing platforms. For the prediction of non-classically secreted proteins, we have used an improved computational strategy, together with homology matching to a dataset of experimentally determined parasitic helminth ES proteins. We applied this protocol to analyse 454 short reads of parasitic nematode,
Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., | 15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates. We evaluate a new maximum likelihood method for estimating allele frequencies in low and medium coverage next-generation sequencing data. The method is based on integrating over uncertainty in the data for each individual rather than first calling genotypes. This method can be applied to directly test for associations in case/control studies. We use simulations to compare the likelihood method to methods based on genotype calling, and show that the likelihood method outperforms the genotype calling methods in terms of: (1) accuracy of allele frequency estimation, (2) accuracy of the
htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists. Availability: Contact: [email protected] Planet E, Stephan-Otto Attolini C, Reina O, Flores O, Rossell D. (2011) htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R. Bioinformatics .
Next generation sequencing (NGS) platforms give researchers much greater power when profiling tumor samples. However, the use of NGS presents challenges surrounding sample variability, platform bias, and potential failure to detect biomarkers. Horizons standards are appropriate for any NGS library preparation including whole-genome, whole-exome, custom capture and targeted amplicon panels. Horizon has developed this Quality-Seq (Q-Seq) NGS Reference Standard range to support the development and continued validation of Next Generation Sequencing platforms. The Tru-Q DNA Reference Standard portfolio covers multiple endogenous SNPs, insertions and deletions. Tru-Q NGS DNA Reference Standard 1 (5% Tier) covers 10 mutations at 5% allelic frequency in genomic DNA format. These may be diluted to even lower allelic frequencies using our Tru-Q 0 Wild Type standard. Furthermore, because the Tru-Q series has 4 different standards at the 5% alleleic frequency range, you may use rotate these as blinded ...
High throughput sequencing technology has been extensively applied in small RNA research. Thousands of miRNAs and their functions have been identified in higher plants. To date, only a single report detailing transcriptome data in celery has been published, and thus, comprehensive miRNA information is not available for this plant [32]. Moreover, there are no reports concerning miRNAs in other species of Apiaceae. In the present study, miRNAs were identified and characterized from two celery varieties, namely, Jinnan Shiqin and Ventura, which come from different geographical sources but have similar morphology. Till now, this study is the first to identify and investigate small RNAs in celery, and the results provide new information for further research into the functions, biological pathways and evolution of target genes related to temperature stresses in celery.. Over six million reads of 16 to 30 nt were obtained from each library. Based on the sequence conservation of mature miRNAs, 418 ...
Hosted by the International Society for Computational Biology (ISCB) and the Centre for Genomic Regulation (CRG), the Next Generation Sequencing Conference 2014 (NGS 2014) is a dedicated meeting on cutting-edge approaches to the processing and analysis of Next Generation Sequencing data. The goal of this conference is to bring together bioinformatics researchers and biologists facing new high-throughput sequencing challenges. The conference will feature presentations showing how current platforms can be used to address key biological questions and what is the current state of the art for data analysis. Sizeable space will also be dedicated to emerging and future trends in high-throughput sequencing and their associated computational challenges.. see more at http://www.iscb.org/ngs2014. ...
Full genomes of several organisms have been sequenced in the past fifteen years, including the human genome in 2004. These studies were completed using Sanger DNA sequencing, which has a limited throughput and high cost meaning the human genome took fifteen years to sequence and cost nearly three billion dollars
CSHL Press publishes monographs, technical manuals, handbooks, review volumes, conference proceedings, scholarly journals and videotapes. These examine important topics in molecular biology, genetics, development, virology, neurobiology, immunology and cancer biology. Manuscripts for books and for journal publication are invited from scientists world wide.
CSHL Press publishes monographs, technical manuals, handbooks, review volumes, conference proceedings, scholarly journals and videotapes. These examine important topics in molecular biology, genetics, development, virology, neurobiology, immunology and cancer biology. Manuscripts for books and for journal publication are invited from scientists world wide.
A novel smartphone-based microscope could make DNA sequence analysis much easier, faster and more readily accessible in remote locations. The dev
View detailed Table of Content here - https://www.marketsandmarkets.com/Market-Reports/ngs-based-rna-seq-market-102977816.html The expression profiling analysis segment accounted for the largest share of the NGS-based RNA-sequencing market, by application, in 2018. Based on application, the NGS-based RNA sequencing market is segmented into expression profiling analysis, small RNA sequencing, De Novo transcriptome assembly, and variant calling & transcriptome epigenetics. In 2018, the expression profiling analysis segment accounted for the largest share of the NGS-based RNA sequencing market. The dominant market position of this segment is attributed mainly to the increasing prevalence of metabolic disorders, multiple sclerosis, and other diseases. These factors will continue to propel the demand for expression profiling analysis to provide specific treatment options in the market during the forecast period.. The nanopore segment is expected to register the highest growth in the NGS-based ...
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus Matthieu Legendre, Stéphane Audic, Olivier Poirot, Pascal Hingamp, Virginie Seltzer, Deborah Byrne, Audrey Lartigue, Magali Lescot, Alain Bernadac, Julie Poulain, Chantal Abergel and Jean-Michel Claverie Published in Advance April 1, 2010, doi:10.1101/gr.102582.109Mimivirus, a virus infecting Acanthamoeba, is the prototype of the…
BACKGROUND Molecular testing of lung adenocarcinomas (ADCs) is crucial for therapy stratification of patients. Because of the often limited diagnostic material, the authors aimed to explore the suitability of cytology smears for next-generation sequencing (NGS) and compared the results with concurrent histological specimens or cell blocks. METHODS A total of 16 formalin-fixed paraffin-embedded (FFPE) ADCs with known genetic alterations were used as the first cohort for targeted DNA and RNA sequencing. In the second cohort of 8 cases, 8 cytological smears were compared with matching histological specimens or cell blocks for the study. For NGS library amplification, commercially available panels for DNA and RNA sequencing were applied. The Ion Torrent Personal Genome Machine and the Ion Reporter workflow (version 5.0) were used for sequencing. RESULTS All DNA libraries derived from FFPE and non-formalin-fixed cytological smear samples produced acceptable quality metrics, thereby enabling ...
Carbon Black is betting on next-generation antivirus technology by acquiring Confer to extend the capability and appeal of its endpoint protection offerings.
Catalyst Biosciences to Host Key Opinion Leader Meeting on Next-Generation Subcutaneous Factor VIIa Marzeptacog Alfa (Activated) in Patients with Bleeding Disorders on August 15 - - South San Francisco (California)
3 credits. Prerequisites: INFO-I 223; and BIOL-N 322 or BIOL-K 322. This course covers basic concepts of genomic sequencing datasets from several sequencing platforms, including how the data motivates computational needs and methods for analysis. Students learn how to devise approaches for analyzing massive clinical and biomedical sequencing datasets and for developing sound hypotheses and predictions from them.. ...
The Illumina MiSeq uses the same established reversible-terminator sequencing by synthesis chemistry as the HiSeq2000. Researchers have a wide range of sequencing read options ranging from 36 bp singleton to 150 bp paired-end reads. The system is capable of generating over 2 Gb data per run with a high percentage of bases over Q30. The high data yield and superior quality allows scientists to conduct a wide variety of sequencing applications including: highly multiplexed PCR amplicon sequencing, small genome sequencing and de novo sequencing, small RNA sequencing, targeted resequencing and 16S metagenomics.. The addition of numerous Illumina MiSeqs adds another level of sequencing for our clients, said Ardy Arianpour, Vice President of Business Development at Ambry Genetics. Our scientists have spent the last couple months validating sequencing runs and getting amazing results so we can deliver and work with multiple types of samples that fit on the MiSeq.. The MiSeq is a fully integrated ...
Liquid biopsy testing utilising Next Generation Sequencing (NGS) is quickly shifting in direction of medical adoption for personalised oncology. However, earlier than NGS can fulfil its potential any novel testing method should establish methods of lowering errors, permitting separation of true low-frequency mutations from procedural artefacts, and be designed to enhance upon present applied sciences. Popular NGS applied sciences sometimes utilise two DNA seize approaches; PCR and ligation, which have recognized limitations and appear to have reached a improvement plateau with solely small, stepwise enhancements being made.. To maximise the final word utility of liquid biopsy testing we now have developed a extremely versatile method to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seqs strengths and versatility keep away from the foremost limitations of each PCR- and ligation-based approaches. This technology is ligation free, easy, environment friendly, versatile, and ...
Dramatic advances in sequencing technologies have opened new possibilities for whole genome analysis. The increasing read length of next-generation sequencing platforms, as well as the promising perspectives of third generation sequencing platforms, will inevitably lead to better assemblies and represent genomes in large stretches of DNA. Also, third generation technologies (such as the PacBio and IonTorrent systems) will be capable of outputting sequencing reads with large undefined inserts, thus providing valuable paired read information for the assembly and scaffolding process. Concurrently, the development of genome closure software should also receive attention to overcome difficult genomic regions that cannot be covered by draft assemblies.. Our results with GapFiller indicate that gapped genomics regions can be reliably closed through an automatic protocol that uses only short sequencing reads. Costly Sanger sequencing can therefore be limited to a few difficult repeat areas. Also, we ...
High-throughput next-generation sequencing (NGS) technologies continue to provide a wealth of sequence information, resulting in significant advances and new discoveries in a wide range of research areas. To enhance your specific NGS-based research and help you achieve your goals, we provide dedicated NGS target enrichment, library preparation and single cell solutions that eliminate bias and deliver uniform coverage. Our streamlined protocols are easy to use and automate seamlessly integrating workflows to use the full power of next-generation sequencing. Together we are making improvements in life possible.
We seek a bioinformatician with computational and analytical skills to join the University of Minnesota Genomics Center (UMGC). The UMGC provides a wide range of innovative genomic services to UMN and external researchers, with a particular focus on next-generation sequencing (NGS). The UMGC operates a fleet of advanced sequencing instruments, including Illumina HiSeq and MiSeq sequencers, a PacBio Sequel sequencer, the 10X Chromium system, and the Fluidigm C1 single-cell system. Through a partnership with the University of Minnesota Supercomputing Institute (MSI), the UMGCs informatics infrastructure is supported by MSIs HPC compute clusters, high-performance storage platforms, and cloud-computing infrastructure. This position in our Informatics group will support the Operations group in providing genomics services to customers, and work with the R&D group to push the limits of the UMGCs instrumentation and put into production the latest advances in sequencing technology.. Required (Minimum) ...
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Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic ...
Deep sequencing analysis of gene expression (DSAGE) measures global gene transcript levels from only 1 to 2 µg total RNA by massively parallel sequencing of cDNA tags
Background: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. Results: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/ human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, ...
The Vironomics Core facilitates research long-read length next generation sequencing. The sequencers in the core are ideal for longer DNA fragment sequencing with instrument run times of only 24 hours. This is accomplished using Ion GeneStudio S5 Prime System, and companion Ion Torrent Chef. The Ion GeneStudio S5 capable of up to 600bp read lengths and has a maximal output of 130 Million 200 bp reads in 12 hours or 4 human exomes per day. Many clients use the longer reads for large genomes, de novo sequencing, 16S sequencing, long amplicons, etc. Customization is available or take advantage of the current expertise in: whole genome sequencing (WGS), de novo assembly, STR cell line verification, targeted amplicon sequencing, plasmid verification, strand-specific RNAseq, and exome sequencing.. ...
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Molecular genetics ; High-Throughput Screening ; Plastic and reconstructive surgery ; Genetics (medical sciences) ; Biology (medical sciences) ; Clinical genetics ; Medical Sciences ; Genetics (life sciences) ; craniosynostosis ; coronal synostosis ; exome sequencing ; high-throughput DNA sequencing ; TCF12-related craniosynostosis ; Saethre-Chotzen syndrome ; genetics ; craniofacial biology ; diagnostic outcomes
Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA. The aim of our study was to compare three library preparation protocols for molecular typing: Nextera XT (Illumina); Nextera Flex (Illumina); and QIAseq FX (Qiagen). We selected 12 ATCC strains from human Gram-positive and Gram-negative pathogens with %G+C-content ranging from 27% (Fusobacterium nucleatum) to 73% (Micrococcus luteus), each having a high quality complete genome assembly available, to allow in-depth analysis of the resulting Illumina sequence data quality. Additionally, we selected isolates from previously analyzed cases of vancomycin-resistant Enterococcus faecium
FFPE and HOPE fixed specimen were comparable in DNA quality for downstream research purposes. Furthermore, FFPE tumor and fresh frozen tumor exome sequencing data, from the same patient, showed an overlap in the SNV analysis. This led to the central aim which included the analysis of somatic copy number alterations (SCNA) using whole exome sequencing on five CRPC and paired normal FFPE samples by the SOLiD4 next generation sequencing platform. The sequencing data identified two genes, YWHAZ and PTK2. Both genes, located on chromosome 8, were amplified on all five sequenced patients. Furthermore, the amplification frequency of both genes increased depending on the stage of PCa: prostate confined or localized PCa, lymph node metastasized PCa and CRPC. YWHAZ knockdown in the PC-3 cell line impaired proliferation and migration. Similarly, PTK2 inhibition, using a pharmacological inhibitor, TAE226 inhibitor, significantly affected both cell migration and proliferation at a concentration of 10 μM. ...
Although genome sequencing has become widely available with the improvements in next-generation sequencing platforms, even with smaller bacterial genomes (the genome of G. xylinus is approximately 3.5Mbp in size), genome sequencing is still relatively unavailable for small to mid-sized research groups due to high costs. We performed a survey of prices offered by all commercially available service providers using the Illumina MiSeq next-generation sequencing platform (which is the most cost-effective method for bacterial genome sequencing) in Europe, and found that the average costs of fully sequencing a 3.5Mbp genome (which includes library preparation, sequencing, bioinformatics and gap filling) is approximately £500.. In order to be able to sequence the genome with the limited budget available to our group, we decided to purchase the necessary materials for library preparation and sequencing run, and perform the full sequencing cycle ourselves, from preparing the sequencing library, to ...
Although genome sequencing has become widely available with the improvements in next-generation sequencing platforms, even with smaller bacterial genomes (the genome of G. xylinus is approximately 3.5Mbp in size), genome sequencing is still relatively unavailable for small to mid-sized research groups due to high costs. We performed a survey of prices offered by all commercially available service providers using the Illumina MiSeq next-generation sequencing platform (which is the most cost-effective method for bacterial genome sequencing) in Europe, and found that the average costs of fully sequencing a 3.5Mbp genome (which includes library preparation, sequencing, bioinformatics and gap filling) is approximately £500.. In order to be able to sequence the genome with the limited budget available to our group, we decided to purchase the necessary materials for library preparation and sequencing run, and perform the full sequencing cycle ourselves, from preparing the sequencing library, to ...
Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16-20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we
RnRMarketResearch.com adds report Next Generation Sequencing (NGS) Market [Platforms (Illumina HiSeq, MiSeq, Life Technologies Ion Proton/PGM, 454 Roche), Bioinformatics (RNA-Seq, ChIP-Seq), (Pyrosequencing, SBS, SMRT), (Diagnostics, Personalized Medicine)] - Global Forecast to 2017 to its store.. The next generation sequencing market is rapidly evolving with a large number of developments taking place to increase accuracy and speed, and reduce costs of sequencing. It is the fastest-growing and most lucrative segment in the genomics space with an estimated growth of 16.3%. The global NGS market was valued at $1.3 billion in 2012 and is poised to reach $2.7 billion by 2017. By supporting genomics research, various government bodies like NHGRI (National Human Genome Research Institute, U.S.) and Biotechnology and Biological Sciences Research Council (BBSRC, U.K.) are increasing the adoption of high-throughput sequencing platforms.. Inquire a Discount @ ...
The Illumina sequencing platform is very popular among next-generation sequencing platforms. However, the DNA sequencing library construction kit provided by Illumina is considerably expensive. The protocol described here can be used to construct high-quality sequencing libraries from chromatin immunoprecipitated DNA. It uses key reagents from third-party vendors and greatly reduces the cost in library construction for Illumina sequencing.
PUNE, India, August 24, 2017 /PRNewswire/ --. According to a new market research report Next-Generation Sequencing (NGS) Services Market by Type (Targeted, RNA-Seq, Exome, De Novo), Technology (Sequencing by Synthesis, Ion semiconductor, SMRT, Nanopore), & Application (Diagnostics, Oncology, Drug Discovery, Agriculture) - Forecasts to 2022, published by MarketsandMarkets(TM), the global market is projected to reach USD 2,748.6 Million by 2022 from USD 1,059.2 Million in 2017; growing at a CAGR of 21.0%. (Logo: http://photos.prnewswire.com/prnh/20160303/792302 ) Browse 56 Market Data Tables and 38 Figures spread through 157 Pages and in-depth TOC on Next-Generation Sequencing (NGS) Services Market http://www.marketsandmarkets.com/Market-Reports/ngs-services-market-194102241.html [http://www.marketsandmarkets.com/Market-Reports/ngs-services-market-194102241.html?utm_source=prnewswire&utm_medium=Refferal&utm_campaign=PaidPR ] Early buyers will receive 10% customization on this report Factors ...
High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating
Next-generation sequencing (NGS) technologies have been widely used in life sciences. However, several kinds of sequencing artifacts, including low-quality reads and contaminating reads, were found to be quite common in raw sequencing data, which compromise downstream analysis. Therefore, quality control (QC) is essential for raw NGS data. However, although a few NGS data quality control tools are publicly available, there are two limitations: First, the processing speed could not cope with the rapid increase of large data volume. Second, with respect to removing the contaminating reads, none of them could identify contaminating sources de novo, and they rely heavily on prior information of the contaminating species, which is usually not available in advance. Here we report QC-Chain, a fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast read processing tool; (2)
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
TY - JOUR. T1 - Characterization of endoscopic ultrasound fine-needle aspiration cytology by targeted next-generation sequencing and theranostic potential. AU - Gleeson, Ferga C.. AU - Kipp, Benjamin R.. AU - Kerr, Sarah E.. AU - Voss, Jesse S.. AU - Lazaridis, Konstantinos N.. AU - Katzka, David A.. AU - Levy, Michael J.. PY - 2015/1/1. Y1 - 2015/1/1. N2 - Determination of tumor genetic architecture based on tissue analysis yields important information on signaling pathways involved in cancer pathogenesis and plays a growing role in choosing the optimal medical management of malignancies. Specifically, the advent of next-generation sequencing has led to a rapidly evolving era of relatively inexpensive, high-throughput DNA sequencing of tumors. One such example is multiplexed tumor genotyping (ie, panel testing) of more than 2800 mutations across 50 commonly mutated cancer-associated genes. This resulting mutational landscape shows medically actionable pathogenic alterations to optimize ...
chnology in a metabarcoding approach, to study aphid food-webs using the cabbage aphid as model. We compared the variations in structure and composition of aphid food-webs in the species native range (United Kingdom, UK) and in an invaded range (New Zealand, NZ). We showed that Illumina MiSeq is a well suited technology to study complex aphid food-webs from aphid mummies. We found an unexpectedly high top down pressure in the NZ cabbage aphid food-web, which coupled to a large ratio of consumer species / prey species and a lack of potential inter-specific competition between primary parasitoids, could cause the NZ food-web to be more vulnerable than the UK one. This study also reports for the first time the occurrence of a new hyperparasitoid species in NZ, as well as new associations between hyperparasitoids parasitoids and the cabbage aphid in this country. We conclude that the complexity of aphid food-webs in agricultural systems could often be underestimated, particularly at higher trophic ...
2012.9.25 Copy number variation detection via normalizing high-throughput sequencing data at a nucleotide level Speaker:Ruibin XI (School of Mathematical Sciences, PKU) Time:1:00pm, Se
Read High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature, Scientific Reports on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid cancers to discover potential therapeutic targets. Here, we describe the results of a clinical NGS panel in patients with advanced melanoma. Thirty-six tumor tissues from patients with BRAF wild-type melanoma at Seoul National University Hospital (SNUH; Seoul, Republic of Korea) were collected and deep-sequenced using the SNUH FIRST-Cancer NGS panel to assess single-nucleotide variants, small insertions/deletions, copy number variations, and structural variations to estimate tumor mutation burden (TMB). We discovered 106 oncogenic alterations and most of the patients (n = 33, 92%) harbored at least one oncogenic alteration, including 2 patients who were initially diagnosed as BRAF V600E-negative but were later confirmed to be positive. Altogether, 36 samples were classified into RAS/BRAF/NF1-mutant (n = 14, 39%) or triple wild-type (n = 22, 61%) melanoma subtypes. The estimated median TMB was 8.2 ...
Highlights:. BRCA1 and BRCA2 analysis by Karyo. BRCA1 and BRCA2 are analyzed using CE-IVD kits in our Next Generation Sequencing platform. Full coverage can be obtained by ordering addition large rearrangement analysis of the two genes by means of MLPA analysis.. Human Breast Cancer Panel by Karyo. 19 genes associated with human breast cancer are analyzed using Next Generation Sequencing. The probes are designed to enrich for all the coding exons and splicing sites of these 19 genes. Copy number variation analysis is also included.. The analyzed genes are: AR, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, DIRAS3, HER2, NBN, PALB2, PTEN, RAD50, RAD51, STK11, TP53, CASP8 και TGFB1.. Exome Analysis - Breast Cancer associated. Hereditary Breast and Ovarian Cancer predominately caused by mutations in genes BRCA1&2 accounts for 5-10% of cases. There is an additional 20-25% with family history present but negative for BRCA1&2 mutations termed Familial Breast Cancer. Modern science has identified ...
Mate Pair Library Sequencing enables the generation of libraries with inserts from 2 to 5 kb in size. These long-insert Paired-End libraries are useful for a number of applications, including De NovoSequencing, genome finishing, and structural variant detection. Combining data generated from Mate Pair library sequencing with that from short-insert paired-end reads provides a powerful combination of read lengths for maximal genomic sequencing coverage across the genome. Following DNA fragmentation, 2-5 Kb fragments are end-repaired with biotin labeled dNTPs. The DNA fragments are circularized, and non-circularized DNA is removed by digestion. Circular DNA is fragmented and fragments biotin labels (corresponding to the ends of the original DNA ligated together) are affinity purified. Purified fragments are end-repaired and ligated to Illumina Paired-End sequencing adapters. Additional sequences complementary to the flow cell oligonucleotides are added to the adapter sequence with tailed PCR ...
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TY - JOUR. T1 - Effective discovery of rare variants by pooled target capture sequencing. T2 - A comparative analysis with individually indexed target capture sequencing. AU - Ryu, Seungjin. AU - Han, Jeehae. AU - Norden-Krichmar, Trina M.. AU - Schork, Nicholas J.. AU - Suh, Yousin. PY - 2018/5/1. Y1 - 2018/5/1. N2 - Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies. In this study, we evaluated the sensitivity and specificity of sequencing for pooled DNA samples of ...
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola ( Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci -QTL- analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 ...
Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference genome or transcriptome is considered a crucial step that remains as one of the most time-consuming. With the steady development of Next Generation Sequencing (NGS) technologies, unprecedented amounts of genomic data introduce significant challenges in terms of storage, processing and downstream analysis. As cost and throughput continue to improve, there is a growing need for new software solutions that minimize the impact of increasing data volume on RNA read alignment. In this work we introduce HSRA, a Big Data tool that takes advantage of the MapReduce programming model to extend the multithreading capabilities of a state-of-the-art spliced read aligner for RNA-seq data (HISAT2) to distributed memory systems such as multi-core clusters or cloud platforms. HSRA has been built ...
Several recent studies from the field of epigenetics have combined chromatin-immunoprecipitation (ChIP) with next-generation high-throughput sequencing technologies to describe the locations of histone post-translational modifications (PTM) and DNA methylation genome-wide. While these reports begin to quench the chromatin biologists thirst for visualizing where in the genome epigenetic marks are placed, they also illustrate several advantages of sequencing based genomics compared to microarray analysis. Accordingly, next-generation sequencing (NGS) technologies are now challenging microarrays as the tool of choice for genome analysis. The increased affordability of comprehensive sequence-based genomic analysis will enable new questions to be addressed in many areas of biology. It is inevitable that massively-parallel sequencing platforms will supercede the microarray for many applications, however, there are niches for microarrays to fill and interestingly we may very well witness a symbiotic ...
Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft.title=Next Generation Sequencing of Extracellular RNA&rft.publisher=The University of Melbourne&rft.description=Exosomes are small nanovesicles released by cells. They can be found in bodily fluids such as blood, milk, saliva and cerebrospinal fluid, and be isolated from cell culture supernatants. Exosomes contain protein and genetic material and have been proposed to play a role in cellular communication whereby their contents can be transferred to other cells. We have shown a role for these vesicles in a number of neurodegenerative disorders such as prion, Alzheimers and Parkinsons diseases. In addition, we have developed a next generation sequencing (NGS) platform to sequence the genetic material contained within these vesicles. The collection contains data from our studies sequencing exosomal RNA from a variety of sources including cell cultures, serum, plasma, milk, urine, CSF both to look at ...
low yield in library preparation - posted in ChIP and Next Generation Sequencing: I got a very successful ChIP (DNA sheared to enrichment around 200 bp, more than 2% input at positive controls). Then I used 10 ng ChIPed DNA to make library for sequencing with the NEB kit. But I got a very poor yield (0.4 ng/ul in 30 ul elutes). I repeated twice with the same DNA and the results didnt turn any better. I used the same kit to make another library two months ago and it worked pretty fine....
Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells. Using more sensitive and specific transcriptome deep sequencing, we compared previously published small miRNA and long mRNA of a set of GC B cells and eBL tumors. MiRWalk2.0 was used to identify the validated target genes for the deregulated miRNAs, which would be important for understanding the regulatory networks associated with eBL development. We found 211 differentially expressed
RNA-Seq data analysis.The CLC Genomics Workbench version 10.1.1 was used for bioinformatics analyses in this study. RNA-Seq analysis was done by mapping next-generation sequencing reads and distributing and counting the reads across genes and transcripts. The latest assembly of the A. aegypti genome (GCF_000004015.4) was used as a reference. All libraries were trimmed from sequencing primers and adapter sequences. Low-quality reads (quality score below 0.05) and reads with more than 2 ambiguous nucleotides were discarded. Clean reads were subjected to an RNA-Seq analysis toolbox for mapping reads to the reference genome with mismatch, insertion, and deletion costs of 2, 3, and 3, respectively. Mapping was performed with stringent criteria and allowed a length fraction of 0.8 in mapping parameter, in which at least 80% of nucleotides in a read must be aligned to the reference genome. The minimum similarity between the aligned region of the read and the reference sequence was set at ...
Beckman Coulters SPRIselect is a SPRI-based chemistry that speeds & simplifies nucleic acid size selection for fragment library preparation for next generation sequencing.
SeqOnce Biosciences has launched its RhinoSeq DNA Library Preparation Kit for next-generation sequencing sample preparation. The firm said that the five tube kit contains preformatted master mixes for a simple, fast, and stable workflow. The tool generates a temporary structure that creates sequence-specific single stranded overhangs for sequencing adaptor litigation. When
Barley (Hordeum vulgare L.) is the one of crucial cereal species used as meals and feed crops, in addition to for malting and alcohol manufacturing. At the top of the final century, conventional breeding methods have been complemented by the use of DNA markers. Molecular markers have additionally been used extensively for molecular genetic mapping and QTL evaluation. In 2012, the barley genome sequencing was accomplished, which offered a broad vary of new alternatives - from a extra environment friendly seek for candidate genes controlling economically vital traits to genomic choice.. The evaluate summarizes the outcomes of the research carried out after barley genome sequencing, which found new areas of barley genetics and breeding with excessive throughput screening and genotyping strategies. During this era, intensive research aimed toward identification of barley genomic loci related to economically vital traits have been carried out; on-line databases and instruments for working with barley ...
PURPOSE: To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants.METHODS: A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000. Exomes of participants were sequenced on an Illumina HiSeq2000. Qualifying variants were rare in the general population (MAF RESULTS: POAG cases showed enrichment of rare variants in camera-type eye development genes (p = 1.40×10-7, corrected p = 3.28×10-4). Implicated eye development genes were related to neuronal or retinal development. HTG cases were significantly enriched for key regulators in the unfolded protein response (UPR) (p = ...
The rapid development of high throughput sequencing (HTS) technologies has made a considerable impact on clinical and genomics research. These technologies offer a time-efficient and cost-effective means for genotyping many pharmaceutical genes affecting the drug response (also known as ADMER genes), which makes HTS a good candidate for assisting the drug treatment and dosage decisions. However, challenges like data storage and transfer, as well as accurate genotype inference in the presence of various structural variations, are still preventing the wider integration of HTS platforms in clinical environments. For these reasons, this thesis presents fast and efficient methods for HTS data compression and accurate ADMER genotyping.First we propose a novel compression technique for reference-aligned HTS data, which utilizes the local assembly technique to assemble the donor genome and eliminate the redundant information about the donor present in the HTS data. Our results show that we can achieve ...
Sequencing genetic material from liquid biopsies promises to be one of the most important recent developments in cancer diagnostics. The relative ease and minimally invasive nature of obtaining liquid biopsies makes it an attractive alternative source of tumor DNA relative to direct tumor biopsies. The importance that
A Survey of Virus Recombination Uncovers Canonical Choices of Artificial Chimeras Generated All through Deep Sequencing Library Preparation. Chimeric reads shall be generated by in vitro recombination all through the preparation of high-throughput sequencing libraries. Our attempt to detect natural recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation bundle revealed that almost all, if not all, detected host-virus chimeras had […]. ...
Minimum Information about a high-throughput nucleotide SEQuencing Experiment. omics Genomics Proteomics Metabolomics This ... producing expressed sequence tags (ESTs). The Sanger method of sequencing was predominant until the advent of high-throughput ... and sequenced using low-throughput, but long read-length methods such as Sanger sequencing. The sequences are then divided back ... Although higher-throughput methods are now used, EST libraries commonly provided sequence information for early microarray ...
This high-throughput method is commonly used in population genetics. SNPs SNPs (single nucleotide polymorphism), are used to ... Sequencing is much faster and more efficient. The analysis is automated, as it uses a technique known as shotgun sequencing. ... Conversely, higher voltages can result in greater band diffusion. Also, if the voltage is too high, the temperature in the ... If a gel has a particularly high number of lanes, then multiple ladders may be placed across the gel for higher clarity. ...
High-throughput sequencing is then used to generate reads containing distinct barcodes that identify the last cDNA nucleotide. ... The isolated RNA is converted into a cDNA library and deep sequenced using high-throughput sequencing technology. Cross-linking ... In 2008 CLIP was combined with high-throughput sequencing (termed "HITS-CLIP") to generate genome-wide protein-RNA interaction ... combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding ...
Other improvements have come from comparing genomic DNA to cDNA sequences and analysis of RNASeq high-throughput data. When ... Many of these changes were single nucleotide insertions or deletions, however several large mis-assemblies have been uncovered ... CDSs have a Sequence Name that is derived from the same Sequence Name as their parent Gene object, so the gene 'F38H4.7' has a ... Sequence curation at WormBase refers to the maintenance and annotation of the primary genomic sequence and a consensus gene set ...
High-throughput next-generation sequencing will be applied. This sample size will be large enough to reliably analyze whole ... 500,000 single nucleotide polymorphism (SNP) markers of a GWAS to 8,000,000 SNP markers and per definition will include ALS- ... study with whole genome sequencing: Phase 1 of Project MinE consists of whole genome sequencing of 300 DNA samples of ALS ... Phase 2 of the project aims to increase the number of whole genome sequenced samples to 22,500, which includes 15,000 ALS ...
The high-throughput sequencing of the methylated DNA fragments produces a large number of short reads (36-50bp or 400 bp, ... In this respect, bisulfite sequencing has much higher resolution (down to a single CpG site; single nucleotide level). However ... Most typical limitations to high-throughput, next generation sequencing apply. The problem of alignment accuracy to repetitive ... Furthermore, DNA detection methods (i.e. array hybridization and high-throughput sequencing) typically involve well established ...
... functional annotation of genetic variants from high-throughput sequencing data". Nucleic Acids Research. 38 (16): e164. doi: ... Single nucleotide polymorphisms (SNPs) play an important role in genome wide association studies because they act as primary ... functional annotation of genetic variants from high-throughput sequencing data". Nucleic Acids Research. 38 (16): e164. doi: ... Single nucleotide variant can also affect the cis-acting regulatory elements in mRNA's to inhibit/promote the translation ...
The most efficient way to find RAD tags is by high-throughput DNA sequencing, called RAD tag sequencing, RAD sequencing, RAD- ... they can be used to identify and genotype DNA sequence polymorphisms mainly in form of single nucleotide polymorphisms (SNPs). ... The use of high-throughput sequencing to analyze RAD tags can be classified as reduced-representation sequencing, which ... More recently, the RAD tag isolation procedure has been modified for use with high-throughput sequencing on the Illumina ...
These high-throughput functional genomics data are derived from experimental data from chips and next-generation sequencing. ... sequence motif Any recurring sequence of nucleotides or amino acids that is or is conjectured to be biologically significant. ... Minimal information about a high-throughput sequencing experiment (MINSEQE) A commercial standard developed by FGED for the ... In nucleic acids, sequence motifs are often short (three to ten nucleotides in length), highly conserved sequences that are ...
Additionally, there is currently no known high throughput technology to make copies of a single protein. Numerous methods are ... Analyzing proteins proves to be more difficult than analyzing nucleic acid sequences. While there are only 4 nucleotides that ... The genomes of viruses and prokaryotes encode a relatively well-defined proteome as each protein can be predicted with high ... On October 16, 2020, the HPP published a high-stringency blueprint covering more than 90% of the predicted protein coding genes ...
New high throughput technologies for DNA sequencing and genomics. 2. Elsevier. pp. 269-304. Schwartz, D. C., et al. "Ordered ... This step is a unique aspect of optical sequencing as it does not actually remove the fluorochrome label of the nucleotide ... Optical sequencing is a single molecule DNA sequencing technique that follows sequence-by-synthesis and uses optical mapping ... Therefore, any sequence reads that are taken from the large template can be mapped onto the genome with a high degree of ...
... for low-throughput sequencing) and 454 Life Sciences (for high-throughput sequencing). The latter platform sequences roughly ... DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been ... Exome sequencing Full genome sequencing Genetic code Pathogenomics RNA-Seq MicroRNA sequencing Sequence motif Wheeler, David A ... While sequencing DNA gives a genetic profile of an organism, sequencing RNA reflects only the sequences that are actively ...
With the advent of the high-throughput DNA and RNA sequence identification methods (such as Illumina sequencing), it became ... possible to efficiently analyse nucleotide sequences of large numbers of relatively short DNA and RNA fragments. Sequences of ... TCP-seq is based on these capabilities of the high-throughput RNA sequencing and further uses the nucleic acid protection ... By sequencing and mapping the fragments back to the source sequence, it is possible to precisely identify the locations and ...
Hi-C uses high-throughput sequencing to find the nucleotide sequence of fragments and uses paired end sequencing, which ... February 2014). "Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment ... Several algorithms have been developed to identify TADs from Hi-C data. Hi-C and its subsequent analyses are evolving. Fit-Hi-C ... There are a number of software tools available for analysis of Hi-C data. DNA motifs are specific short DNA sequences, often 8- ...
In contrast, the high-throughput sequencing technologies used in exome sequencing directly provide the nucleotide sequences of ... The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology. The goal of this approach is ... By using exome sequencing, fixed-cost studies can sequence samples to much higher depth than could be achieved with whole ... Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding ...
DNA nanoball sequencing is a type of high throughput sequencing technology used to determine the entire genomic sequence of an ... RNA sequencing was one of the earliest forms of nucleotide sequencing. The major landmark of RNA sequencing is the sequence of ... The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that parallelize ... and low-purity samples and yields high-quality sequencing data. The high-throughput nature of current DNA/RNA sequencing ...
"Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories". Nature Biotechnology. 31(11):1015-1022. ... Small RNAs are noncoding RNA molecules between 20 and 200 nucleotide in length. The item "small RNA" is a rather arbitrary term ... Small RNA-Seq can analyze thousands of small RNA molecules with a high throughput and specificity. The greatest advantage of ... Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate ...
The throughput is currently lower than that of other high-throughput sequencing technologies, although the developers hope to ... sequencing can occur in real-time. In reality, the sequencing rate is limited by the cycling of substrate nucleotides through ... Ion semiconductor sequencing may also be referred to as Ion Torrent sequencing, pH-mediated sequencing, silicon sequencing, or ... microbial transcriptome sequencing, targeted sequencing, amplicon sequencing, or for quality testing of sequencing libraries. ...
... is a high throughput sequencing technology that is used to determine the entire genomic sequence of an ... Fluorescent nucleotides bind to complementary nucleotides and are then polymerized to anchor sequences bound to known sequences ... refined DNA nanoball sequencing to sequence nucleotide samples on their own platform. DNA Nanoball Sequencing involves ... They were able to identify over 50,000 single nucleotide variants. Roach et al. used DNA nanoball sequencing to sequence the ...
DNA nanoball sequencing[edit]. Main article: DNA nanoball sequencing. DNA nanoball sequencing is a type of high throughput ... RNA sequencing was one of the earliest forms of nucleotide sequencing. The major landmark of RNA sequencing is the sequence of ... The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that parallelize ... High-throughput sequencing (HTS) methods[edit]. Several new methods for DNA sequencing were developed in the mid to late 1990s ...
In both bulk high-throughput sequencing and FISSEQ, short sequences are locally amplified and then imaged one nucleotide at a ... with a sequence of colors corresponding to the nucleotide sequence of the parent molecule. The nucleotide sequence of each DNA ... high-throughput readout of sequence and spatial information. Nucleoside triphosphate Polony sequencing Mitra RD, Shendure J, ... Fluorescent in situ sequencing (FISSEQ) is a method of sequencing a cell's RNA while it remains in tissue or culture using next ...
... is an efficient and high-throughput technique for analyzing the genome-wide methylation profiles on a single nucleotide level. ... High-throughput bisulfite sequencing in mammalian genomes. Methods. 48: 226-232. Harris, Alan et al. 2010. "Comparison of ... Sequencing: The fragments are then sequenced. When RRBS was first developed, Sanger sequencing was initially used. Now, next ... For Illumina sequencing, 36-base single-end sequencing reads are most commonly performed. Sequence alignment and analysis: Due ...
... method and high-throughput sequencing (e.g., ). The canonical DNA nucleotides include 2 purines (A and G) and 2 pyrimidines (T ... They think it may be caused by the mutation rate in the Y-linked sequence higher than the X-linked sequence mutation rate. The ... the total rate of transversions for a sequence may be higher even when the rate of transitions is higher on a per-path basis. ... These C-to-T nucleotide substitutions occur 10-50 times faster than that at rest sites in DNA sequences, especially likely ...
... the human genome and the recent advent of high throughput sequencing and genome-wide association studies of single nucleotide ... There were 21 higher medical specialty institutions that offered diploma degrees so in total, there were 147 higher medical and ... to improve health care via any combination of higher quality, higher efficiency (spurring lower cost and thus greater ... China has also been improving its higher education in regards to health informatics. At the end of 2002, there were 77 medical ...
Illumina sells a number of high-throughput DNA sequencing systems, also known as DNA sequencers, based on technology developed ... Illumina began offering single nucleotide polymorphism (SNP) genotyping services in 2001 and launched its first system, the ... Young, Susan (2014-01-14). "Illumina Claims It's Reached $1,000-Genome Milestone with New High-Throughput Human Genome ... "Illumina drops sequencing price to $4,000 - UTSanDiego.com". Everygenome.com: Individual genome sequencing - Illumina, Inc. ...
Wan, KH; Yu, C; George, RA; Carlson, JW; Hoskins, RA; Svirskas, R; Stapleton, M; Celniker, SE (2006). "High-throughput plasmid ... the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the ... each nucleotide is not across from its opposite) and determines the stability of the sequences to be together. Furthermore, ... MiRNAs are formed from longer sequences of RNA that are cut free by a Dicer enzyme from an RNA sequence that is from a ...
Sequence read archive: high-throughput sequencing data. *Cancer Chromosomes: cytogenetic databases. *PubChem BioAssay: ... Nucleotide: sequence database (GenBank). *Protein: sequence database. *Genome: whole genome sequences and mapping ... Probe: sequence-specific reagents. *NLM Catalog: NLM bibliographic data for over 1.2 million journals, books, audiovisuals, ... The Entrez system can provide views of gene and protein sequences and chromosome maps. Some textbooks are also available online ...
... (ASV) is a term used to refer to single DNA sequences recovered from a high-throughput marker gene ... of the DNA sequence. ASV methods on the other hand are able to resolve sequence differences by as little as a single nucleotide ... Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences". The ISME Journal. 9 (4): 968-979 ... Whereas ASVs are exact nucleotide sequence variation, so the changes seen between past experiments can be more easily traced to ...
Research has focused on combinatorial chemistry, genomic mining, omic technologies and high throughput screening. As the cost ... genotyping or exome or whole genome sequencing. Sequencing provides many more data points, including detection of mutations ... Similarly, hypersensitivity to the antiretroviral drug abacavir is strongly associated with a single-nucleotide polymorphism ... The higher prevalence of central nervous system side effects in African as compared to American and European patients treated ...
"Identification of biologically active PDE11-selective inhibitors using a yeast-based high-throughput screen". Chem. Biol. 19 (1 ... Sanger Centre, The; Washington University Genome Sequencing Cente, The (1999). "Toward a complete human genome sequence". ... 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP to the corresponding 5'- ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
人類基因組含有許多不同的調控序列,並以此來控制基因表現。這些序列是典型的短序列,會出現在靠近基因的位置。由於高通量表達(high-throughput expression;指利用電腦與機器輔助以進行大量的序列分析)技術與比較基因組學研究的出現,人們開始 ... Genoscope and Whitehead announce a high sequence coverage of the Tetraodon
Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput ... The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their ... Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences.[4] ... Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation. ...
"Methods for High-Content, High-Throughput Image-Based Cell Screening" (PDF). Proceedings of the Workshop on Microscopic Image ... "Nucleotide sequence of bacteriophage λ DNA". Journal of Molecular Biology 162 (4). Arquivado dende o orixinal o 02 de decembro ... C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". ... Chimpanzee Sequencing and Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human ...
High-throughput technique ("-omics"). DNA microarray. Mass spectrometry. Lab-on-a-chip. ... functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms ... A high-throughput study, which denotes technology that looks at extensive genetic markers, focused on epigenetic differences ... Epigenetics is the study of stable heritable changes in gene function that do not involve changes in the DNA sequence.[1] The ...
... which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), ... Sequence profiling tools can find restriction enzyme sites, open reading frames in nucleotide sequences, and predict secondary ... Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this ... Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of ...
"High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes". ... Single-nucleotide polymorphisms (SNPs), which are a big part of genetic variation in the human genome, and copy number ... Single cell sequencing examines the sequence information from individual cells with optimized next-generation sequencing (NGS) ... specific sequences may be transcribed inefficiently, thus causing sequence drop-out or generating incomplete sequences.[1][40] ...
"Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics". Current Genomics. 17 (6): 460-475 ... Transfer DNA binary system Barker, R. F.; Idler, K. B.; Thompson, D. V.; Kemp, J. D. (1983-11-01). "Nucleotide sequence of the ... Gielen, J.; Terryn, N.; Villarroel, R.; Van Montagu, M. (1999-08-01). "Complete nucleotide sequence of the T-DNA region of the ... C Koncz, N Martini, R Mayerhofer, Z Koncz-Kalman, H Körber, G P Redei, and J Schell (1989). "High-frequency T-DNA-mediated gene ...
Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan ... "High-throughput functional annotation and data mining with the Blast2GO suite". Nucleic Acids Research. 36 (10): 3420-35. doi: ... Inferred from Sequence Similarity (ISS) means a human curator has reviewed the output from a sequence similarity search and ... AmiGO Slimmer Archived 2011-09-29 at the Wayback Machine; maps granular annotations up to high-level terms ...
... most known deoxyribozyme sequences have been discovered through a high-throughput in vitro selection technique, similar to ... The 10-23 DNAzyme contains a 15-nucleotide catalytic core that is flanked by two substrate recognition domains. This DNAzyme ... DNA is more cost-effective, and DNA can be made with longer sequence length and can be made with higher purity in solid-phase ... The initial pool for in vitro evolution can be derived from a narrowed subset of sequence space, such as a certain round of an ...
This strategy was developed in the 1980s for sequencing whole genomes before high throughput techniques for sequencing were ... February 1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature. 265 (5596): 687-95. doi:10.1038/265687a0. PMID ... Whole genome shotgun sequencing is another method of genome sequencing that does not require a library of high-capacity vectors ... A high resolution map can be created by sequencing both ends of inserts from several clones in a genomic library. This map ...
Research in this field has led to the use of high-throughput measurement. High throughput measurement allows for the gathering ... Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan. ... Homology is the study of biological structures and nucleotide sequences in different organisms that come from a common ancestor ... "Genome Sequencing to the Rest of Us". Scientific American.. *^ a b c Koonin, Eugene (6 March 2001). "Computational Genomics". ...
sequence-specific mRNA binding. • ربط حمض نووي. • ربط بروتيني. • RNA binding. • nucleotide binding. ... 2005). "High-throughput mapping of a dynamic signaling network in mammalian cells". Science. 307 (5715): 1621-5. Bibcode: ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur.441.. ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Next-generation sequencing (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing ... The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between ... New high-throughput sequencing technologies are dramatically lowering the cost of DNA sequencing, with many researchers hoping ... Genetic information exists in the sequence of these nucleotides, and genes exist as stretches of sequence along the DNA chain.[ ...
Zhang XHD (2011). Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi ... RNA interference has an important role in defending cells against parasitic nucleotide sequences - viruses and transposons. It ... The type of RNA editing that is most prevalent in higher eukaryotes converts adenosine nucleotides into inosine in dsRNAs via ... Janitz M, Vanhecke D, Lehrach H (2006). "High-Throughput RNA Interference in Functional Genomics". RNA Towards Medicine. ...
Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta ... which only considered small numbers of exonic single nucleotide polymorphisms (SNPs) and did not investigate sex-specific ... "A draft sequence of the Neandertal genome". Science. 328 (5979): 710-722. Bibcode:2010Sci...328..710G. doi:10.1126/science. ... a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.[33][34][35] ...
Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi Research. ISBN 978-0- ... double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals". Cell 101 (1): 25-33. PMID ... transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences". Mol Microbiol 6 ( ... A investigación da RNAi a escala xenómica depende da tecnoloxía do cribado ou rastreo de alto rendemento (HTS, High-throughput ...
The process of finding a new drug against a chosen target for a particular disease usually involves high-throughput screening ( ... After sequencing of the human genome allowed rapid cloning and synthesis of large quantities of purified proteins, it has ... Discovery and development of nucleoside and nucleotide reverse transcriptase inhibitors. *Discovery and development of Bcr-Abl ... much higher in natural compounds), structure rigidity (higher in natural compounds) and number of aromatic moieties (higher in ...
By direct sequencing with high-throughput sequencing techniques (next-generation sequencing, i.e. pyrosequencing), hundred ... to produce 11-nucleotide 'tag' fragments. These tags are concatenated and sequenced using long-read Sanger sequencing ( ... The cDNA concatemers can then be isolated and sequenced using modern high-throughput DNA sequencers, and these sequences can be ... LongSAGE was a more robust version of the original SAGE developed in 2002 which had a higher throughput, using 20 μg of mRNA to ...
2005). "High-throughput mapping of a dynamic signaling network in mammalian cells". Science. 307 (5715): 1621-5. doi:10.1126/ ... nucleotide binding. • ubiquitin conjugating enzyme activity. • ubiquitin-protein transferase activity. • transferase activity. ... 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... 2004). "Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins ...
The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that parallelize ... "The complete nucleotide sequence of the mitochondrial genome of Tetraodon nigroviridis". DNA Sequence. 17 (2): 115-21. doi: ... High-throughput sequencingEdit. See also: Illumina dye sequencing and Ion semiconductor sequencing ... In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis operations may be run in parallel.[55][56] ...
Wang, X; Liu, S (2011). "Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data ... Mir-2 hairpin precursor sequences are highly conserved, in particular in their 3' arm in which the first 10 nucleotides are ... Mir-13 subfamily emerged from mir-2 sequences before the insect radiation. Although mir-11 and mir-6 have similar sequences to ... One mir-2 microRNA in Drosophila, dme-miR-2a-2 [1], is two nucleotides offset with respect to the canonical products of other ...
Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta ... nucleotide binding. • microfilament motor activity. • protein binding. • ADP binding. • protein membrane anchor. • actin- ... "The DNA sequence of human chromosome 22". Nature. 402 (6761): 489-95. doi:10.1038/990031. PMID 10591208.. ... a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.[80][81][82] ...
Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan ... Thisse high-throughput gene expression analysis[4]).. Information in ZFIN is tightly linked to the web resources of the ... a high throughput expression analysis". ZFIN Direct Data Submission (Unpublished).. CS1 maint: uses authors parameter (link) ... Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information ...
... multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): 1792-97. doi:10.1093/nar/ ... For nucleotide sequences a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches ... sequences of S. {\displaystyle S}. until the modified sequences, S. i. ′. {\displaystyle S_{i}^{'}}. , all conform to length L ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ...
Although the rise of higher throughput and cost-effective single-nucleotide polymorphism (SNP) platforms led to the era of the ... but still higher than in actual gene sequences. In addition, microsatellite sequencing and ISSR sequencing are mutually ... Because microsatellites consist of such repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence ... of proteins contain repeating sequences of amino acids encoded by short sequence repeats.[23] Most of the short sequence ...
"Bioinformatics High Throughput Sequence Search and Analysis (white paper)". GenomeQuest. Archived from the original on May 13, ... Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan. ... be the sequences to be aligned, where n. {\displaystyle n}. and m. {\displaystyle m}. are the lengths of A. {\displaystyle A}. ... being the length of the shorter sequence.. Gap penalty example[edit]. Take the alignment of sequences TACGGGCCCGCTAC. and ...
"Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics. 7: 270. doi:10.1186/1471-2105-7-270. PMC ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. ...
The throughput is currently lower than that of other high-throughput sequencing technologies, although the developers hope to ... sequencing can occur in real-time. In reality, the sequencing rate is limited by the cycling of substrate nucleotides through ... Ion semiconductor sequencing may also be referred to as Ion Torrent sequencing, pH-mediated sequencing, silicon sequencing, or ... microbial transcriptome sequencing, targeted sequencing, amplicon sequencing, or for quality testing of sequencing libraries.[3 ...
NCBI nucleotide data We searched ChimerDB 2.0 (32) to obtain the GenBank accession IDs of the publicly available sequences that ... R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Vinay K. ... Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008;40 ... these high-throughput methodologies involve the massively parallel sequencing of millions of copies of fragments of cellular ...
Here, we describe PHLI-seq, a novel approach that enables high-throughput isolation and genome-wide sequence analysis of single ... By applying PHLI-seq, we reveal the heterogeneity of breast cancer tissues at a high resolution and map the genomic landscape ... Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to ... To investigate more genomic differences at the single nucleotide level, we performed whole-exome sequencing (WES) for 11 ...
... a data analysis pipeline enabling the quantification of nucleotide conversions in high-throughput sequencing datasets. We ... The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized ... masking to uncouple true SNPs from nucleotide conversions to facilitate a robust and sensitive quantification of nucleotide- ... SLAM-DUNK provides both raw counts of nucleotide-conversion containing reads as well as a base-content and read coverage ...
... easy to use primer design webtool capable of generating high-quality targeted resequencing assays. The workflow is fully ... High-Throughput Nucleotide Sequencing / methods* * Humans * Plants / genetics * Plants / metabolism * Polymerase Chain Reaction ... High-throughput PCR assay design for targeted resequencing using primerXL BMC Bioinformatics. 2017 Sep 6;18(1):400. doi: ... Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing ...
computer-aided design; coronavirus infections; disease transmission; evolution; high-throughput nucleotide sequencing; ... Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants ... Nucleotide positions showing nucleotides that differed from the consensus were tabulated. Colored dots indicate nucleotide ... The sequences of the 3 genomes were aligned, and differences between the sequence of England/Qatar/2012 and England1 (upper row ...
Genome sequencing projects by organism. Nucleotide DNA and RNA sequences. SRA High-throughput sequence reads ... The most up-to-date set of SARS‑CoV‑2 nucleotide and protein sequences ... Protein sequences, 3-D structures, and tools for the study of functional protein domains and active sites ... Gene sequences and annotations used as references for the study of orthologs structure, expression, and evolution ...
... in DNA or gene sequencing. In particular, it will discuss DNA sequencing technology and software and... ... Using mRNA in DNA Sequencing This article looks at the usage and development of messenger Ribonucleic Acid (mRNA) ... Single Nucleotide Polymorphisms. They are able to do this thanks to analyzing single nucleotide polymorphisms (SNP). These SNPs ... Using High-Throughput Sequencing Technology for mRNA and DNA Sequencing. By DoctorZeus Nov 29, 2010 ...
Oligonucleotide Array Sequence Analysis * Polymorphism, Single Nucleotide * RNA, Long Noncoding* * Regulatory Sequences, ... Keywords: CD247; ENCODE; UCSC genome browser; cis-regulatory sequence; high-throughput sequencing; lncRNA. ... In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements ... Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from ...
Nucleotide sequence accession numbers.The sequences determined in this study have been deposited in the NCBI Sequence Read ... Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data. Shaokang Zhang, Yanlong Yin, Marcus B. ... Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data. Shaokang Zhang, Yanlong Yin, Marcus B. ... Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data. Shaokang Zhang, Yanlong Yin, Marcus B. ...
The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data Authors: Yan Guo, ... Critical region within 22q11.2 linked to higher rate of autism spectrum disorder Authors: Caitlin C. Clements, Tara L. Wenger, ...
Molecular Sequence Data. Databases, Genetic. High-Throughput Nucleotide Sequencing. Massively-Parallel Sequencing. ... Morash M, Mitchell H, Beltran H, Elemento O, Pathak J. The Role of Next-Generation Sequencing in Precision Medicine: A Review ... comparison of Life Technologys Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet. 2013 Oct;132(10): ...
Molecular Sequence Data. Databases, Genetic. High-Throughput Nucleotide Sequencing. Massively-Parallel Sequencing. ... Any patient whose tumor has been sequencing using a multiplex method such as next-generation sequencing including hot-spot, ... Morash M, Mitchell H, Beltran H, Elemento O, Pathak J. The Role of Next-Generation Sequencing in Precision Medicine: A Review ... Any patient whose tumor has been tested for transcriptomic characteristics such as RNA sequencing ...
Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red ... Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red ... Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red ... After aligning sequence to the bovine reference genome build UMD 3.0 and binning reads into one Mbp groups; reads were ...
2012.9.25 Copy number variation detection via normalizing high-throughput sequencing data at a nucleotide level Speaker:Ruibin ... 2012.9.25 Copy number variation detection via normalizing high-throughput sequencing data at a nucleotide level. 2019-07-08 21: ... 2012.9.25 Copy number variation detection via normalizing high-throughput sequencing data at a nucleotide level ... In recent years, the advancement of high-throughput sequencing (HTS) technologies has provided an opportunity for CNV detection ...
High-throughput nucleotide library sequencing. WO2017053902A1. 23 Sep 2016. 30 Mar 2017. Abvitro Llc. High throughput process ... Methods for high throughput genotyping. US20080241831 *. 28 Mar 2007. 2 Oct 2008. Jian-Bing Fan. Methods for detecting small ... High throughput microarray spotting system and method. US20050106621 *. 27 Dic 2004. 19 May 2005. Winegarden Neil A.. Devices ... Methods for high throughput genotyping. US8039817. 1 May 2009. 18 Oct 2011. Illumina, Inc.. Compensator for multiple surface ...
The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ... Croix River Virus (SCRV) sequences. We also observed many reads that were homologous to microbial and/or pathogenic isolates, ... As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that ... Croix River Virus (SCRV) sequences. We also observed many reads that were homologous to microbial and/or pathogenic isolates, ...
High-Throughput Nucleotide Sequencing; Medication Adherence; Metagenome; Metagenomics; Patient Compliance; Proteobacteria; Risk ... Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant ... In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in ... The most important risk factor for ESBL-PE colonization was travel destination, and the highest colonization rate was found in ...
We precisely designed 244,000 DNA sequences implementing 56 replicates of a full factorial design to evaluate nucleotide, ... For each sequence, we measured reporter transcript abundance and decay, polysome profiles, protein production and growth rates ... Associations between designed sequences properties and these consequent phenotypes were dominated by secondary structures and ... Comparative analyses of natural and mutated sequences have been used to probe mechanisms of gene expression, but small sample ...
... we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms ... With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent ... thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. Furthermore, ... using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). ...
Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is ... gemBS: high throughput processing for DNA methylation data from bisulfite sequencing. Bioinformatics 35(5), 737-742 (2018). ... The corresponding FASTQ, BAM and VCF files were deposited in European Nucleotide Archive (ENA) with with study ID PRJEB1752911. ... Whole genome sequencing and whole genome bisulfite sequencing data are freely available from the ENA under the project ID ...
... improve the sequencing capacity by several orders of magnitude [38]. High-throughput DNA sequencing (HTS), thus provided the ... 100 nucleotides long, on average). Applied to Neanderthals, HTS first delivered one megabase of nuclear sequence information [ ... d) The high-throughput sequencing revolution. The Roche-454 platform replaced bacterial colonies by PCR colonies, which are ... 2015 Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol. Ecol. Resour. 16, ...
These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are ... Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid ... High-Throughput Nucleotide Sequencing / standards* * Humans * Laboratories / standards* * Reproducibility of Results * Sequence ... ACMG clinical laboratory standards for next-generation sequencing Genet Med. 2013 Sep;15(9):733-47. doi: 10.1038/gim.2013.92. ...
Our high-throughput DNA analysis technique will have application in. *verifying DNA sequencing data ... In our technique, we first amplify a target DNA sequence using stable-isotope-labeled nucleotides and then compare the masses ... High-Throughput Genotyping for Medical Diagnostics and Gene Discovery. Features. Our analytical technique determines the ... Supports high-throughput analyses for examining large numbers of proteins. *Provides a fluorescent indicator proportional to ...
Single Nucleotide Polymorphism (SNP) Genotyping: Higher sample throughput; Outstanding data quality; Dramatically lower costs ... Sequencing library preparation using amplicon tagging. *Copy Number Variation: High-resolution CNV studies using digital PCR • ... A high-throughput antibody-based technique with procedures similar to that of Western blots ... Gene Expression: High throughput (9,000 qPCR reactions)• Low cost • Compatibility with existing reagents ...
High-Throughput Nucleotide Sequencing. *Missense Mutation. *BRCA1. *Molecular Sequence Data. *Case-Control Studies ... Germline single nucleotide polymorphisms in ERBB3 and BARD1 genes result in a worse relapse free survival response for HER2- ... Higher BARD1 and BRCA1 expression is associated with worse prognosis of early breast cancer patients, especially the ones that ... Among high hereditary risk Chinese BC patients, 23.8% contained germline mutations, including 6.8% in non-BRCA1/2 genes. TP53 ...
High-throughput Nucleotide Sequencing. Techniques of nucleotide sequence analysis that increase the range, complexity, ... and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation ... High Throughput Drug Sensitivity Assay and Genomics- Guided Treatment of Patients With Relapsed or Refractory Acute Leukemia ... This clinical trial studies the feasibility of choosing treatment based on a high throughput ex vivo drug sensitivity assay in ...
High-throughput nucleotide sequencing. Insulin-like growth factor I/genetics. Mutation/genetics. Receptor IGF type 1 /genetics ... or exome sequencing. We sequenced 80 patients, and had a mean coverage of 354x, with more than 99% of the target region with > ... Targeted gene panel sequencing is a useful technology for the diagnosis of children born small for gestational age ... The main goal of this project is to apply the technology of massive parallel sequencing to comprehend growth disturbs in ...
High-Throughput Nucleotide Sequencing. *NOTCH1. *Squamous Cell Carcinoma. *Whole Exome Sequencing. *Suppressor of Cytokine ... By combining whole-genome sequencing, SNP array, RNA sequencing, and FISH analyses, we defined a 1q23.1 biallelic minimally ... There was high consistency between the results of NGS-PCR technique and routine ARMS-PCR in KRAS and BRAF mutation detection. ... However, higher JAG1 expression was found in MCPyV-negative than in MCPyV-positive MCC (p. CONCLUSION: Expression of NOTCH3, as ...
High-throughput Nucleotide Sequencing. Techniques of nucleotide sequence analysis that increase the range, complexity, ... DNA sequencing DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA ... and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation ... Single-cell RNA sequencing (scRNA-seq) is a powerful tool to study immune cells, which enables an unbiased way to discover ...
High-throughput nucleotide sequencing. Lipoatrophic. Monogenic diabetes. Neonatal diabetes mellitus. Wolfram syndrome. ... Objectives: (1) to develop a customized targeted massively parallel sequencing panel to sequence the rare types of monogenic ... Genetic research of index cases was done by massively parallel sequencing. Family segregation and confirmation of the variants ... Targeted massively parallel sequencing for rare monogenic diabetes forms and inherited lipodystrophy ...
  • We demonstrate using experimentally generated and simulated datasets that DUNK allows constant mapping rates irrespective of nucleotide-conversion rates, promotes the recovery of multimapping reads and employs Single Nucleotide Polymorphism (SNP) masking to uncouple true SNPs from nucleotide conversions to facilitate a robust and sensitive quantification of nucleotide-conversions. (biomedcentral.com)
  • Secondly, Single Nucleotide Polymorphisms (SNPs) in the genome will lead to an overestimation of nucleotide-conversions if not appropriately separated from experimentally introduced genuine nucleotide conversions. (biomedcentral.com)
  • These SNPs are the changes in the nucleotide basis (A,T,C and G) and the human body is believed to contain millions of SNPs. (infobarrel.com)
  • New high throuput technologies can now analyze hundreds of thousands of SNPs, which should allow the scientist greater understanding of genetic differences that cause diseases.In this way, scientists can identify who is at risk and also get closer to cracking the genetic code of the disease. (infobarrel.com)
  • While public datasets currently annotate 4,527 SNPs between the two strains in this interval, thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. (biomedcentral.com)
  • With the recent completion of the Perlegen/NIEHS mouse resequencing [ 1 ], over ten million mouse single nucleotide polymorphisms (SNPs) are now annotated in the public databases, resulting in a dramatic increase in the genome-wide knowledge of variation among 16 of the most widely used mouse strains. (biomedcentral.com)
  • one of them is the rapid advancement in high‐throughput single nucleotide polymorphisms (SNPs) genotyping technologies which has enabled researchers to comprehensively interrogate the entire human genome. (els.net)
  • The most prominent feature of these high‐throughput genotyping platforms is the ability to interrogate several hundred thousands to one million SNPs simultaneously in a microarray. (els.net)
  • The paradigm shift in genetic approach to GWAS has been attributed to several important developments, notably the rapid advancement in high‐throughput SNPs genotyping technologies. (els.net)
  • High‐throughput SNPs genotyping technologies had enabled researchers to interrogate several hundred thousands to one million SNPs simultaneously in a microarray. (els.net)
  • In this candidate gene study, we have identified novel associations between six validated single nucleotide polymorphisms (SNPs) spanning a 97.6 kb region within the bovine guanine nucleotide-binding protein Gs subunit alpha gene ( GNAS ) domain on bovine chromosome 13 and genetic merit for a range of performance traits in 848 progeny-tested Holstein-Friesian sires. (springer.com)
  • For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. (biomedcentral.com)
  • Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. (biomedcentral.com)
  • Single nucleotide polymorphisms (SNPs) were identified for TaSnRK2.9 -5A, while no polymorphism was identified in TaSnRK2.9 -5B and TaSnRK2.9 -5D. (springer.com)
  • We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). (plos.org)
  • Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. (hindawi.com)
  • 3) high-throughput (HTP) sequence-based markers: SNPs [ 3 ]. (hindawi.com)
  • A search for single nucleotide polymorphisms (SNPs) identified 2,487 candidate SNPs distributed among 1,265 transcripts. (unl.edu)
  • To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is PCR-amplified and subjected to heteroduplex formation, followed by CEL I cleavage. (psu.edu)
  • Exact SNPs are then deter-mined by sequencing. (psu.edu)
  • Moreover, single nucleotide polymorphisms (SNPs) are valuable genetic markers to use for gene discovery, population studies, and individual identification. (bio-medicine.org)
  • ABSTRACT: Single Nucleotide Polymorphisms (SNPs) are the most common and abundant genetic variation found in the genome of any living species, from bacteria to humans. (scirp.org)
  • We report here a cost-effective high-resolution melting-based genotyping method for the screening of 27 canonical SNPs that includes these new diagnostic markers. (scirp.org)
  • If we look closer at the DNA genes, we see that every gene is contains a base of adenine (A), thymine (T), cytosine (C), and guanine (G). The order of these bases on their phosphate backbone governs their DNA sequence. (infobarrel.com)
  • The RING motif is a cysteine-rich sequence found in a variety of proteins that regulate cell growth, including the products of tumor suppressor genes and dominant protooncogenes. (cancerindex.org)
  • We used the Sure Select technology (Agilent Technologies, CA, USA) to study approximately 390 genes chosen by participate of the IGFs/IGF1R system, or genes already associated with growth disorders, or candidate genes found in previous studies of aCGH (Array Comparative Genomic Hybridization) or exome sequencing. (usp.br)
  • Next-generation sequencing technologies provide an excellent opportunity to screen large numbers of individuals with a diagnosis of diabetes for mutations in disease-associated genes. (biomedcentral.com)
  • We utilized a targeted sequencing approach using the Illumina HiSeq to perform a case-control sequencing study of 22 monogenic diabetes genes in 4016 individuals with type 2 diabetes (including 1346 individuals diagnosed before the age of 40 years) and 2872 controls. (biomedcentral.com)
  • Targeted sequencing of genes linked with monogenic diabetes can identify disease-relevant mutations in individuals diagnosed with type 2 diabetes not suspected of having monogenic forms of the disease. (biomedcentral.com)
  • thus, sequencing of all monogenic diabetes genes should be routinely considered in such individuals. (biomedcentral.com)
  • Substantial intrastrain variation at the nucleotide level complicates molecular and genetic studies in zebrafish, such as the use of CRISPRs or morpholinos to inactivate genes. (genetics.org)
  • Aligning nucleotide sequences is a key requisite when searching for homologous genes. (mdpi.com)
  • In 2008, two human transcriptomes, composed of millions of transcript-derived sequences covering 16,000 genes, were published, and by 2015 transcriptomes had been published for hundreds of individuals. (wikipedia.org)
  • 2018 ). Therefore, breeding for high grain yield is the utmost objective and there is continuous search for genes underpinning yield and its direct contributing traits. (springer.com)
  • Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. (whiterose.ac.uk)
  • More recently, next-generation sequencing has become available, with the advantage that several genes can be simultaneously analyzed where necessary, eg, for discrimination of possible type 2N VWD or mild hemophilia A. Additionally, several techniques can now identify deletions/duplications of an exon or more that result in VWD including multiplex ligation-dependent probe amplification and microarray analysis. (whiterose.ac.uk)
  • Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. (biomedcentral.com)
  • This review provides a comprehensive summary of the recent advances in identification of candidate genes variations, targeted approaches to high-risk neuroblastoma and evaluates the methods utilized for detection, which will provide new avenues to develop therapies and further genetic researches. (pubmedcentralcanada.ca)
  • Based on the molecular beacon technology, we developed a series of Mx4000 molecular beacon allelic discrimination kits , ff for the detection of single or multiple nucleotide changes in human genes. (bio-medicine.org)
  • Sequence analysis of the E6 and E7 genes was also carried out in the same cervical samples in order to confirm the association between nucleotide sequence variations in the HPV16 E1 ORF and HPV16 variant lineages. (deepdyve.com)
  • A phylogenetic tree of the E1 ORF and nucleotide sequence analysis of the E1, E6 and E7 genes revealed that intratypic nucleotide sequence polymorphisms located in the E1 ORF can be used to identify the major phylogenetic branch to which a HPV16 genome belongs. (deepdyve.com)
  • These included single nucleotide point mutations in well-characterized cancer genes such as mTOR, MLL2, CDKN2C, and PIK3CA. (bcgsc.ca)
  • Previous studies in other mammalian species have shown that DNA sequence variation within the imprinted GNAS gene cluster contributes to several physiological and metabolic disorders, including obesity in humans and mice. (springer.com)
  • 3. Abstract Next generation genomic sequencing technologies have been instrumental in significantly accelerating biological research and discovery of genomes for humans, mice, snakes, plants, bacteria, virus, cancer cells, and so on. (slideshare.net)
  • 4. Introduction: DNA and RNA sequencing applications Genetic concepts and interesting facts All humans, animals, plants, and living organisms are comprised of cells. (slideshare.net)
  • CAP allows for testing on humans to animals, and is one of the highest accreditations a laboratory can receive. (operon.com)
  • The sequences of the 3 genomes were aligned, and differences between the sequence of England/Qatar/2012 and England1 (upper row) or EMC/2012 and England1 (lower row) were tabulated. (nih.gov)
  • At present, 1100 subjects have successfully enrolled in the project, and over a hundred of them have had their genomes sequenced. (nature.com)
  • Full genomes of several organisms have been sequenced in the past fifteen years, including the human genome in 2004. (news-medical.net)
  • In 2014, a new generation of Illumina Genome Analyzer was created that can efficiently sequence 45 human genomes a day for 1000 US dollars each. (news-medical.net)
  • This approach is widely used in the assembly of whole genomes but cannot be applied to targeted enrichment protocols, as hybridization-based capture methods for massively parallel sequencing typically require small insert fragments (200 bp)[ 5 ] and breakpoints of structural variants may lie outside of targeted regions. (biomedcentral.com)
  • Genomic sequence sampling: A strategy to high resolution sequence‐based physical mapping of complex genomes. (currentprotocols.com)
  • Edition 2021-02-19 (77) selected specimens underwent sequencing and Nexstrain phylogenetic analysis along with 1,480 globally representative genomes present in GISAID as of January 11, 2021. (cdc.gov)
  • Lesions IN Genomes) exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small indel mismatches. (psu.edu)
  • Performing whole-genome sequencing on AAA patients and controls, we demonstrated its predictive precision solely from personal genomes. (stanford.edu)
  • 2005). Confounding this issue, eukaryotic genomes are far less gene-dense than those of bacteria and archaea, meaning that equivalent sequencing efforts will yield much more information for prokaryotes. (deepseanews.com)
  • Mismatches in reads yielded from standard sequencing protocols such as genome sequencing and RNA-Seq originate either from genetic variations or sequencing errors and are typically ignored by standard mapping approaches. (biomedcentral.com)
  • For genetic improvement, using genomic tools, an ordered array of DNA variants and associated flanking sequence across the genome is required. (haldanessieve.org)
  • This warrants full genomic sequencing of the mouse strains used as genetic models. (biomedcentral.com)
  • 1 × 10(7) wild-type nucleotides, thereby enabling the study of heterogeneous populations and very-low-frequency genetic alterations. (nih.gov)
  • Genetic research of index cases was done by massively parallel sequencing. (usp.br)
  • Conclusions: A customized targeted massively parallel sequencing panel allowed genetic diagnosis of rare types of monogenic diabetes, with a positivity of 23/42 cases analyzed, being possible to perform the genotype-phenotype correlation. (usp.br)
  • Diabetes mellitus is a heterogeneous disorder characterized by high fasting blood glucose levels or hyperglycemia that results from a combination of both genetic and environmental risk factors. (biomedcentral.com)
  • The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. (g3journal.org)
  • The clinical molecular laboratory, which carries both CLIA and CAP accreditations, offers molecular genetics services such as DNA extraction, identification and validation of public and proprietary genetic variants, real-time PCR assay design and validation, Sangers sequencing with ABI3730xl high throughput instruments and customized clinical reporting. (operon.com)
  • Typical projects includeo DNA extraction, identification and validation of public and proprietary genetic variants, real-time PCR assay design and validation, Sangers sequencing with ABI3730xl high throughput instruments and customized clinical reporting. (operon.com)
  • Although this mechanism has been known since the 1980s, the genetic basis for nucleotide insertions has remained unclear. (nextbio.com)
  • Polymerase chain reaction and Sanger sequencing have been mainstays of genetic analysis for several years. (whiterose.ac.uk)
  • The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis. (biomedcentral.com)
  • By the application of high-throughput DNA sequencing techniques, it is possible to identify the variants that cause genetic disorders. (news-medical.net)
  • Single pass sequencing and physical and genetic mapping of human brain cDNAs. (currentprotocols.com)
  • The history of the genetic sequence databases. (currentprotocols.com)
  • This study establishes a high-throughput transcriptome and genetic-marker infrastructure. (plos.org)
  • 2014) Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity. (plos.org)
  • Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. (nih.gov)
  • This work provides significant genetic resources for studying S. albicosta and demonstrates the power of applying of second-generation sequencing to previously understudied species. (unl.edu)
  • Many of the sequence changes have been identified as the cause of monogenic disorders or are associated with a genetic predisposition to multifactorial diseases including cancer and cardiovascular and infectious diseases. (bio-medicine.org)
  • The sequence changes also constitute the genetic basis for many nondisease traits, such as obesity and a persons response to drugs. (bio-medicine.org)
  • SNP Genotyping Markets: Single base pair mutations that occur at a specific site in the DNA sequence, the most common type of genetic variation between human beings. (marketresearch.com)
  • Every study churning out millions of DNA sequences is analyzing less than 1% of the genetic material in a sample. (deepseanews.com)
  • Moreover, because the heterogeneous subclones were sequenced in a pool, the detection sensitivity of variants with a low-level allele fraction was low. (biomedcentral.com)
  • Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. (nih.gov)
  • To assist clinical laboratories with the validation of next-generation sequencing methods and platforms, the ongoing monitoring of next-generation sequencing testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics has developed the following professional standards and guidelines. (nih.gov)
  • Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families. (cancerindex.org)
  • Cancer is characterized by intra-tumor heterogeneity, the presence of distinct cell populations with distinct complements of somatic mutations, which include single-nucleotide variants (SNVs) and copy. (bioportfolio.com)
  • We analyzed protein-coding variants identified from the sequence data and compared the frequencies of pathogenic variants (protein-truncating variants and missense variants) between the cases and controls. (biomedcentral.com)
  • Within this strain, we have identified the majority of the genome that matches the reference sequence and documented most of the variants. (genetics.org)
  • This strain has utility for many reasons, but in particular it will be useful for any researcher who needs to know the exact sequence (with all variants) of a particular genomic region or who wants to be able to robustly map sequences back to a genome with all possible variants defined. (genetics.org)
  • Therefore, it is preferable to carry out studies in a zebrafish strain in which the regions of invariant sequence are known with a high degree of confidence and all variants are categorized to allow for robust genomic mapping. (genetics.org)
  • 10 million previously unreported single-nucleotide variants (SNVs). (genetics.org)
  • However, these methods were largely overtaken by high throughput sequencing of entire transcripts, which provided additional information on transcript structure such as splice variants. (wikipedia.org)
  • Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. (medworm.com)
  • Detection of genomic variants of SARS-CoV-2 circulating in wastewater by high-throughput sequencing. (cdc.gov)
  • Wastewater sequencing facilitates real-time detection of emerging variants of SARS-CoV-2 that might be missed by sequencing of samples from individuals seen in clinical settings. (cdc.gov)
  • Although massively parallel sequencing instruments are in principle well suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. (pnas.org)
  • As a result, three possible allelic combinations of two sequence variants (Allele 1/Allele 1, Allele 2/Allele 2, Allele 1/Allele 2) can be distinguished simultaneously in a DNA sample. (bio-medicine.org)
  • Stratagenes Mx4000 molecular beacon allelic discrimination kits include the following components: a mixture of two allele-specific molecular beacons with an exact sequence match to each of the two target sequence variants, three genotype-specific DNA controls corresponding to the homozygotes and the heterozygote of the two sequence variants, target-specific PCR primers, and an optimized PCR buffer. (bio-medicine.org)
  • By using two different molecular beacons in each PCR reaction, three possible allelic combinations (genotypes) of two sequence variants can be distinguished simultaneously by the type of fluorescence detected: TET fluorescence indicates homozygosity for the wild-type allele, FAM fluorescence indicates homozygosity for the mutant allele, and both TET and FAM fluorescence together indicates heterozygosity ( Figure 2 ). (bio-medicine.org)
  • Analysis of the E1 ORF revealed 27 nucleotide changes, and these changes were correlated with those found in HPV16 Asian American and African type II variants. (deepdyve.com)
  • Very conveniently, the polymerase chain reaction (PCR) technique had just been developed to amplify minute amounts of specific genomic targets up to a level compatible with downstream sequencing [ 14 ]. (royalsocietypublishing.org)
  • Polymerase chain reaction (PCR)-based WGA introduces sequence-dependent bias because of the exponential amplification with random primers ( 17 , 18 , 22 ). (sciencemag.org)
  • It uses an optimized design criteria relaxation cascade and a thorough downstream in silico evaluation process to generate high quality singleplex PCR assays, reducing the need for amplicon normalization, and outperforming other target enrichment strategies and similar primer design tools when considering assay quality, coverage uniformity and target coverage. (nih.gov)
  • In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients. (biomedcentral.com)
  • Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. (biomedcentral.com)
  • however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. (biomedcentral.com)
  • The LRPS assay is a sensitive, high-throughput technique with potential application to routine genotyping of MTBC in sputum samples from TB patients. (biomedcentral.com)
  • Commonly known as the OLA, the Oligonucleotide Ligation Assay is an analyte specific reagent (ASR) that is centered around the hybridization of a PCR primer with an exact match to a target sequence. (thefreedictionary.com)
  • The oligonucleotide ligation assay (OLA) relies on hybridization with specific oligonucleotide probes that can effectively discriminate between the wild-type and variant sequences. (thefreedictionary.com)
  • Agrawal et al (2011) whole-exome sequencing and gene copy number analyses to study 32 primary hesd and neck squamous cell tumors and found that nearly 40% of 28 mutations identified in NOTCH1 were predicted to truncate the gene product, suggesting that NOTCH1 may function as a tumor suppressor gene rather than an oncogene in HNSCC. (cancerindex.org)
  • Using the same templates on both platforms, we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms and samples. (biomedcentral.com)
  • In the present study, three copies of TaSnRK2.9 were isolated from chromosomes 5A, 5B and 5D of wheat ( Triticum aestivum L.). The coding regions of TaSnRK2.9 -5A, TaSnRK2.9 -5B and promoter region of TaSnRK2.9 -5D were investigated for sequence polymorphism. (springer.com)
  • Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data. (semanticscholar.org)
  • 2008) Single Nucleotide Polymorphism Typing of Bacillus anthracis from Sverdlovsk Tissue. (scirp.org)
  • Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China. (frontiersin.org)
  • We sequenced the two most commonly used inbred mouse strains, DBA/2J and C57BL/6J, across a region of chromosome 1 (171.6 - 174.6 megabases) using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). (biomedcentral.com)
  • There are several platforms for massively parallel DNA sequencing currently on the market [ 2 ], and we took this opportunity to directly compare the same dataset on two of the three most widely used platforms: Illumina (Genome Analyzer) and Applied Biosystems (SOLiD). (biomedcentral.com)
  • Currently, the three next‐generation sequencing platforms are Illumina® Genome Analyzer, Roche® 454 GS‐FLX Sequencer and ABI® SOLiD Sequencer. (els.net)
  • The Sanger method of sequencing was predominant until the advent of high-throughput methods such as sequencing by synthesis (Solexa/Illumina). (wikipedia.org)
  • The Illumina Genome Analyzer also has a sequencing-by-synthesis concept where the reaction is stopped after each base, a fluorescent dye is used to read the base label and the sequence reaction is then continued with the next base. (news-medical.net)
  • Another technique is Ion Torrent and Ion proton sequencing, which unlike Roche/453 and Illumina techniques does not use optical signals during sequencing. (news-medical.net)
  • Multiplex 16S rDNA (V3-V4) sequencing of bacterial DNA was performed with the Illumina MiSeq platform. (diva-portal.org)
  • The transcriptome of adult male S. albicosta was partially sequenced using Illumina sequencing-by-synthesis. (unl.edu)
  • Since 2004 when next-generation sequencing platforms such as 454 , Illumina and SOLiD really took off, scientists have amassed ~400 billion base pairs of microbial DNA-so, in 7 years we've looked at only 3% of the nucleotides present in 1 milliliter of seawater. (deepseanews.com)
  • After the adapters are ligated to both ends of the small RNAs, retrotranscription occurs producing complementary DNA molecules (cDNAs) which will be, eventually, amplified by different amplification techniques depending on the sequencing protocol that is being followed (Ion Torrent exploits the emulsion PCR, while Illumina requires a bridge PCR) in order to obtain up to billions of amplicons to be sequenced. (wikipedia.org)
  • That is why AFLP markers are still popular in molecular genetics research in crops with little to zero reference genome sequence available [ 12 ]. (hindawi.com)
  • Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear amplification and sequencing) to generate a spatiotemporal gene expression map of the Caenorhabditis elegans syncytial germline from adult hermaphrodites and males. (genetics.org)
  • This is accomplished by washing away the synthesized sequence, repeating the bridge amplification cycle for the reverse of the strand, removing the starting strand and adding a new sequencing primer for the second read. (news-medical.net)
  • However, there is a high background error rate because the production of the library and flow cell requires in vitro amplification steps. (news-medical.net)
  • Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in low genome coverage. (sciencemag.org)
  • Here, we report on a new amplification method-multiple annealing and looping-based amplification cycles (MALBAC)-that offers high uniformity across the genome. (sciencemag.org)
  • These methods have relied on whole-genome amplification (WGA) of an individual cell to generate enough DNA for sequencing ( 17 - 21 ). (sciencemag.org)
  • Five cycles of preamplification are followed by exponential amplification of the full amplicons by PCR to generate micrograms of DNA required for next-generation sequencing ( Fig. 1 ). (sciencemag.org)
  • The keys to this approach, called the Safe - Seq uencing S ystem ("Safe-SeqS"), are ( i ) assignment of a unique identifier (UID) to each template molecule, ( ii ) amplification of each uniquely tagged template molecule to create UID families, and ( iii ) redundant sequencing of the amplification products. (pnas.org)
  • Moreover, amplification of the E1 ORF revealed a disruption between nucleotides 878 and 1523 in five high- and two low-grade cervical cases, indicating that integration of HPV DNA occurs at an early stage of viral infection. (deepdyve.com)
  • PRPF8 mutations are generally missense and scattered throughout the gene (Figure 1A,D). The high level of conservation between the yeast Prp8 and human PRPF8 proteins allows for precise mapping of homologous mutations (Figure 1D). (nih.gov)
  • We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. (biomedcentral.com)
  • In recent years, the advancement of high-throughput sequencing (HTS) technologies has provided an opportunity for CNV detection with unprecedented resolution. (echenfeng.com)
  • Here, we developed an algorithm that can normalize HTS data at a nucleotide level as well as a CNV detection algorithm based on the normalized HTS data that can detect CNVs with base-pair level resolution. (echenfeng.com)
  • Short read aligners are well suited to single nucleotide and indel detection. (biomedcentral.com)
  • Here we describe a method that combines CNV detection through high-resolution depth of coverage analysis with call confirmation through partially-mapped reads. (biomedcentral.com)
  • Evolution of molecular markers has been primarily driven by the throughput and cost of detection method and the level of reproducibility [ 6 ]. (hindawi.com)
  • Invention of PCR technology and the application of this method for the rapid detection of polymorphisms overthrew low-throughput RFLP markers, and new generation of PCR-based markers emerged in the beginning of nineties. (hindawi.com)
  • The rapid expansion in the quantity and quality of RNA-Seq data requires the development of sophisticated high-performance bioinformatics tools capable of rapidly transforming this data into meaningful information that is easily interpretable by biologists. (pubmedcentralcanada.ca)
  • Contemporary sequencing platforms can generate megabytes to gigabytes of data in a single sequencing run ( 10 ). (pubmedcentralcanada.ca)
  • This magnitude of data not only allows for the characterization of moderate to high abundant transcripts, it also provides sufficient coverage and depth to characterize rare and potentially novel low abundant transcripts that went undetected by earlier methodologies. (pubmedcentralcanada.ca)
  • Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. (biomedcentral.com)
  • However, the huge amounts of sequencing data cannot be connected to the spatial and phenotypic histopathological information because the tissue-comprising cells must be pooled or dissociated in solution before sequencing. (biomedcentral.com)
  • Here, we present Digital Unmasking of Nucleotide conversions in K-mers (DUNK), a data analysis pipeline enabling the quantification of nucleotide conversions in high-throughput sequencing datasets. (biomedcentral.com)
  • Identifying nucleotide conversions in high-throughput sequencing data comes with two major challenges: First, depending on nucleotide conversion rates, reads will contain a high proportion of mismatches with respect to a reference genome, causing common aligners to misalign them to an incorrect genomic position or to fail aligning them at all [ 7 ]. (biomedcentral.com)
  • In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. (nih.gov)
  • Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. (asm.org)
  • SeqSero ( www.denglab.info/SeqSero ) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. (asm.org)
  • In total, 28 Gbp of sequence data were generated from seven Cervus elaphus (European red deer and Canadian elk) individuals. (haldanessieve.org)
  • The resultant sRNA library data revealed that the surveyed tick populations produced reads that were homologous to St. Croix River Virus (SCRV) sequences. (frontiersin.org)
  • In this review, we will first present how the technology underlying the characterization of ancient hominin sequence data developed in the past 30 years. (royalsocietypublishing.org)
  • While all five PGP centres generate whole-genome sequencing (WGS), some PGPs, such as PGP-UK, produce additional multi-omics data. (nature.com)
  • DNA sequencing is then performed followed by data analysis. (nature.com)
  • For this cohort, we collected whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) in addition to WGS and 450 k data. (nature.com)
  • CHEMIN gathers high-resolution data from less than a milligram of sample material. (lanl.gov)
  • SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. (bioportfolio.com)
  • In this protocol, we provide a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and the H3K36me3 mark with broad enrichment. (biomedsearch.com)
  • The algorithm requires ∼3 GB of RAM and 1.5 h of computing time to analyze a ChIP-seq data set containing 30 million reads, an estimate that increases with sequence coverage. (biomedsearch.com)
  • The raw sequence data have been deposited in the NCBI Sequence Read Archive [BioProject ID: 246102]. (genetics.org)
  • This review focuses on the comparative genomics of non-coding RNAs in the context of new sequencing technologies and especially dealing with two extremely important and timely research aspects: the development of new methods to align RNAs and the analysis of high-throughput data. (mdpi.com)
  • class contains data from short-read sequences, including sequence headers, nucleotide sequences, and the quality scores for the sequences. (mathworks.com)
  • This data is typically obtained from a high-throughput sequencing instrument. (mathworks.com)
  • object from short-read sequence data. (mathworks.com)
  • Use the object properties and methods to explore, access, filter, and manipulate all or a subset of the data, before doing subsequent analyses or sequence alignment and mapping. (mathworks.com)
  • Access to genomic data from DNA and ribonucleic acid (RNA) sequences is configured on IBM Storwize V7000 Unified or SONAS Gateway solutions. (slideshare.net)
  • Genome coverage and nucleotide sequence identity of the full genome or several contigs in relation to the OvPV reference genome strain OvPV/Wales/2017/S014175 (International Nucleotide Sequence Data Collaboration accession no. (cdc.gov)
  • Mutation confirmation for Next-Generation Sequencing data as well as other genomic technologies. (operon.com)
  • Algorithms based on next-generation sequencing data can also identify missing or duplicated regions. (whiterose.ac.uk)
  • This allows for twice the amount of sequenced data to be generated. (news-medical.net)
  • We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. (biomedcentral.com)
  • Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. (biomedcentral.com)
  • In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. (biomedcentral.com)
  • Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner. (biomedcentral.com)
  • Paired-end mapping methods perform well for mate-pair sequence data and have the advantage of identifying both balanced (e.g. translocations or inversions) and unbalanced (deletions and duplications) structural variation. (biomedcentral.com)
  • Depth of coverage methods have achieved higher signal to noise by averaging data across a genomic region[ 6 - 8 ], however, doing so results in a loss of the ability to detect smaller mutations. (biomedcentral.com)
  • By combining these orthologous approaches, CNVs of any size can be identified from targeted high-throughput sequence data with a low false-positive rate. (biomedcentral.com)
  • Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. (semanticscholar.org)
  • Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. (medworm.com)
  • This unit provides an overview of biomedical information resources, focusing on sequence data, structure information, and the associated literature, and also discusses how nucleotide sequence data gets into the databases in the first place. (currentprotocols.com)
  • It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time. (gnu.org)
  • We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs. (mdpi.com)
  • In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. (stanford.edu)
  • Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data. (stanford.edu)
  • In this work, we describe an orthogonal method for filtering Ig-seq data, which considers the structural viability of each sequence. (jimmunol.org)
  • Handbook of Nucleic Acid Sequences. (currentprotocols.com)
  • The subject apparatus, systems, and chips are particularly suited for performing polymerase chain reactions on thousands of nucleic acid sequences, up to and including sequences of an entire genome of an organism of interest. (google.ca)
  • The demand is growing in the clinical research field for high-throughput screening methodologies that are sensitive enough to distinguish nucleic acid sequences differing by a few or one nucleotide. (bio-medicine.org)
  • Commonly referred to as 'RNA-Seq', these high-throughput methodologies involve the massively parallel sequencing of millions of copies of fragments of cellular transcripts ( 11 ). (pubmedcentralcanada.ca)
  • 2008) Identification of somatically acquired rearrangements in cancer using genome‐wide massively parallel paired‐end sequencing. (els.net)
  • We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. (pnas.org)
  • Massively parallel sequencing represents a particularly powerful form of digital PCR in that hundreds of millions of template molecules can be analyzed one by one. (pnas.org)
  • In the 1980s, low-throughput sequencing using the Sanger method was used to sequence random transcripts, producing expressed sequence tags (ESTs). (wikipedia.org)
  • In 1995, one of the earliest sequencing-based transcriptomic methods was developed, serial analysis of gene expression (SAGE), which worked by Sanger sequencing of concatenated random transcript fragments. (wikipedia.org)
  • High-throughput genotyping and Sanger sequencing for clinical trials. (operon.com)
  • These studies were completed using Sanger DNA sequencing, which has a limited throughput and high cost meaning the human genome took fifteen years to sequence and cost nearly three billion dollars. (news-medical.net)
  • Therefore electrophoresis, as used in Sanger sequencing, is not needed to generate a nucleotide read out of the output. (news-medical.net)
  • While this type of sequencing is faster and cheaper than Sanger sequencing, there is a known issue of homopolymer errors where there is a difficulty in distinguishing a run of bases in a sequence that are identical, such as the sequence GGGG ( i.e. the guanine quartet). (news-medical.net)
  • Here, we describe PHLI-seq, a novel approach that enables high-throughput isolation and genome-wide sequence analysis of single cells or small numbers of cells to construct genomic maps within cancer tissue in relation to the images or phenotypes of the cells. (biomedcentral.com)
  • Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. (nih.gov)
  • As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that were identified. (frontiersin.org)
  • The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ticks and other vector species. (frontiersin.org)
  • Analysis of V H sequences of genomic DNA by 454 deep sequencing of four HIV-1 Env-reactive clonal lineages from AHI subjects did not reveal any unmutated lineage members. (rupress.org)
  • Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. (bioportfolio.com)
  • For analysis by HTS, 6 DNA samples extracted from cutaneous swabs obtained from the skin surface of facial areas (forehead and eyebrows) of patients previously studied by PCR for MCPyV sequences were selected ( 5 ). (cdc.gov)
  • A variant of SAGE using high-throughput sequencing techniques, called digital gene expression analysis, was also briefly used. (wikipedia.org)
  • Overexpressing transgenic rice also showed higher grains per spike which is in accordance with association analysis results. (springer.com)
  • The use of short unique sequence indexes, or barcodes, increases sequencing throughput and allows analysis of multiple samples in a single sequencing run. (biomedcentral.com)
  • Computational analysis of DNA and protein sequences. (currentprotocols.com)
  • Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. (currentprotocols.com)
  • In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods. (google.com)
  • Contigs with sequence similarities to several nucleorhabdoviruses were identified by high-throughput sequencing analysis from a black currant (Ribes nigrum L.) cultivar. (usda.gov)
  • However, the rapid developments of sequencing technologies have started replacing the microarray experiments for both structural and functional genomics studies. (els.net)
  • Thanks to deep-sequencing, tracking natural selection through population genomics is becoming the status quo. (deepseanews.com)
  • ESTs came to prominence during the 1990s as an efficient method to determine the gene content of an organism without sequencing the entire genome. (wikipedia.org)
  • With the advent of next generation sequencing (NGS) technologies, affordable solutions are now available to get access to the complete genome sequence of an organism. (scirp.org)
  • This article looks at the usage and development of messenger Ribonucleic Acid (mRNA) in DNA or gene sequencing. (infobarrel.com)
  • The mRNA is therefore a partial copy of the sequence of the DNA. (infobarrel.com)
  • The first attempt at capturing a partial human transcriptome was published in 1991 and reported 609 mRNA sequences from the human brain. (wikipedia.org)
  • Molecular cloning and sequencing provided a new dimension to the field, as they allowed the type of mutation, rather than simply its presence, to be identified ( 19 - 24 ). (pnas.org)
  • They are able to do this thanks to analyzing single nucleotide polymorphisms (SNP). (infobarrel.com)
  • Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. (biomedcentral.com)
  • With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses. (biomedcentral.com)
  • With the advent of next-generation, high-throughput sequencing (HTS), we are now in a position to determine to what extent polymorphisms remain cryptic (either undiscovered or not previously annotated as a SNP in a specific strain comparison) in various mouse models and assess their impact on downstream analyses. (biomedcentral.com)
  • 2004) Selecting a maximally informative set of single‐nucleotide polymorphisms for association analyses using linkage disequilibrium. (els.net)
  • By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. (sciencemag.org)
  • The variations occurring in these chromosomes, such as single-nucleotide variations (SNVs) and copy-number variations (CNVs) ( 3 ), are the driving forces in biological processes such as evolution and cancer. (sciencemag.org)
  • DNA was extracted from tissues from an approximately 2400-year-old Egyptian mummy, and a multicopy 3.4 kb Alu element was sequenced following bacterial cloning. (royalsocietypublishing.org)
  • Moreover, depending on the nucleotide-conversion efficiency and the number of available conversion-sites, high sequencing depth is required to reliably detect nucleotide-conversions at lower frequencies. (biomedcentral.com)
  • Sequencing approach has been quickly adopted for various applications in structural and functional genomic studies, for example, ChIP‐Seq, transcriptome profiling (RNA‐Seq) and paired‐end sequencing method to detect structural variations. (els.net)
  • The nucleotide additions release a light signal that can then detect the location and sequence of the nucleotide being incorporated. (news-medical.net)
  • The ability to detect the full spectrum of mutations is critical to the success of targeted sequencing projects. (biomedcentral.com)
  • Currently, the common method used to detect cleaved products is by polyacryl-amide gel electrophoresis using a high-throughput genotyping platform. (psu.edu)
  • Detect Single Nucleotide Sequence Changes with Mx4000 Molecular Beacon,,,Allelic Discrimination Kits ( Allelic discrim. (bio-medicine.org)
  • High-Throughput Transcriptome Sequencing for SNP and Gene Discovery i" by Nicholas J. Miller, Jing Sun et al. (unl.edu)
  • Variant confirmation next generation sequencing. (nih.gov)
  • Many of the NGS sequencing protocols rely on the production of a genomic library that contains thousands of fragments of the target nucleic acids that will then be sequenced by proper technologies. (wikipedia.org)
  • We cloned and sequenced several individual fragments from this library, all of which were products formed by ligation of multiple mutant RNA linker oligonucleotides. (asm.org)
  • If my life were an SAT analogy, it would be Dr Bik:Sequencing platforms as Teenage Girls:Twilight. (deepseanews.com)
  • PrimerXL is an state-of-the-art, easy to use primer design webtool capable of generating high-quality targeted resequencing assays. (nih.gov)
  • Next generation sequencing (NGS) has facilitated genome and transcriptome analyses of several stone fruit trees. (usda.gov)
  • Comparative analyses of natural and mutated sequences have been used to probe mechanisms of gene expression, but small sample sizes may produce biased outcomes. (nature.com)
  • Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. (nature.com)
  • For high-throughput genotyping, two kompetitive allele-specific PCR (KASP) markers were developed. (springer.com)
  • Next generation sequencing combined with an existing bovine reference genome enabled the deer genome to be assembled sufficiently for large-scale SNP discovery. (haldanessieve.org)
  • While transcriptomics was first heralded by the introduction of microarray technologies over two decades ago ( 8 , 9 ), the field is currently undergoing revolutionary expansion by virtue of the application of deep-sequencing technologies for the quantitative and qualitative characterization of cellular transcripts ( 10 ). (pubmedcentralcanada.ca)
  • SLAM-DUNK provides both raw counts of nucleotide-conversion containing reads as well as a base-content and read coverage normalized approach for estimating the fractions of labeled transcripts as readout. (biomedcentral.com)
  • Associations between designed sequences properties and these consequent phenotypes were dominated by secondary structures and their interactions within transcripts. (nature.com)
  • There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA-Seq, which uses high-throughput sequencing to record all transcripts. (wikipedia.org)
  • A total of 238 nucleotide substitutions and 6 deletions were found in SARS-CoV-2 isolates. (cdc.gov)
  • Moreover for many non-coding RNAs, evolution is likely to be mostly constrained at the structural level and not at the sequence level. (mdpi.com)
  • A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. (mdpi.com)
  • Small RNAs are noncoding RNA molecules between 20 and 200 nucleotide in length. (wikipedia.org)
  • Most recently, emerging sequencing technologies further expanded the potential readout of nucleotide-conversions in high-throughput sequencing datasets by employing chemoselective modifications to modified nucleotides in RNA species, resulting in specific nucleotide conversions upon reverse transcription and sequencing [ 3 ]. (biomedcentral.com)
  • Beyond providing a readily accessible tool for analyzing SLAMseq and related time-resolved RNA sequencing methods (TimeLapse-seq, TUC-seq), DUNK establishes a broadly applicable strategy for quantifying nucleotide conversions. (biomedcentral.com)
  • Depth of coverage methods do not require breakpoint capture or have specific size restrictions, yet such methods are hampered by low signal to noise ratio due to sparse sampling (a product of low overall coverage) and sampling bias based on sequence GC-content, bait coverage, and other factors affecting capture efficiency. (biomedcentral.com)
  • Integration of nucleic acid sequencing into the routine mycobacteriology laboratory and use of the MicroSeq 500 microbial identification system and Mayo Clinic databases containing additional genotypes of common species and added species significantly reduced the number of organisms that could not be identified by phenotypic methods. (asm.org)
  • Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. (stanford.edu)
  • Computational error-correction methods use sequence information alone, primarily designating sequences as likely to be correct if they are observed frequently. (jimmunol.org)
  • We also show how ABOSS is able to identify structurally impossible sequences missed by other error-correction methods. (jimmunol.org)
  • Instead of sequencing the genomic DNA of cells from different subclones in a tumor mass separately, these approaches relied upon computational inference to separate subclones from the mixed population. (biomedcentral.com)
  • Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine. (nih.gov)
  • These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are being made. (nih.gov)
  • Next-generation sequencing technologies are also facilitating further advances in therapeutic decision making and disease prediction for at-risk patients. (nih.gov)
  • Single-cell transcriptomics technologies provide high-dimensional assessment of the transcriptional states of immune cells and have been successfully applied to discover new immune cell types, reveal haematopoietic lineages, identify gene modules dictating immune responses and investigate lymphocyte antigen receptor diversity. (bioportfolio.com)
  • In this review, we discuss the impact and applications of single-cell RNA sequencing technologies in immunology. (bioportfolio.com)
  • Expeditious developments of sequencing technologies have started threatening the market of microarray. (els.net)
  • Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. (stanford.edu)
  • The Nordic Environmental Nucleotide Network aims to help groups further develop and refine the use of molecular based technologies by avoiding redundancy of effort and facilitating rapid dissemination and implementation of advances. (nordforsk.org)
  • Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate and get information about noncoding RNA molecules in order to evaluate and discover new forms of small RNA and to predict their possible functions. (wikipedia.org)
  • Mutational landscapes of the primary and recurrent tumour specimens were analysed using high-throughput sequencing technologies. (bcgsc.ca)
  • The onset of next-generation HTS enabled us to obtain full sequence coverage of a region of chromosome 1 in the D2 and B6 mouse strains. (biomedcentral.com)
  • Prompted by rapid progress in next-generation sequencing techniques ( 11 ), there have been several reports on whole-genome sequencing of single cells ( 12 - 16 ). (sciencemag.org)
  • Next-generation sequencing of the Ig gene repertoire (Ig-seq) produces large volumes of information at the nucleotide sequence level. (jimmunol.org)
  • In a SNP-based genome-wide association study, Capasso et al (2009) reported that common variations in BARD1 influence susceptibility to high-risk neuroblastoma. (cancerindex.org)
  • After RNA isolation, chemical nucleotide-analog derivatization specifically modifies thiol-containing residues, which leads to specific misincorporation of guanine (G) instead of adenine (A) when the reverse transcriptase encounters an alkylated 4SU residue during RNA to cDNA conversion. (biomedcentral.com)
  • RPCH interacted with RPCHR with extremely high sensitivity (EC 50 20 pM). (frontiersin.org)
  • Moreover, these mice exhibited higher sensitivity to DSB-inducing drugs. (bmj.com)
  • Although AFLPs are anonymous too, the level of their reproducibility and sensitivity is very high owing to the longer +1 and +3 selective primers and the presence of discriminatory nucleotides at 3′ end of each primer. (hindawi.com)
  • Assembly of the sequence reads yielded 16,847 transcript sequences, of which 6,631 could be assigned a putative function. (unl.edu)
  • For each sequence, we measured reporter transcript abundance and decay, polysome profiles, protein production and growth rates. (nature.com)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for protein and DNA/RNA. (gnu.org)
  • The frequencies of somatic mutations were relatively high in these gp41-reactive antibodies. (rupress.org)
  • Number (proportion) of OvPV reads in the complete high-throughput sequencing dataset. (cdc.gov)