A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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.
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 relationships of groups of organisms as reflected by their genetic makeup.
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.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
The functional hereditary units of BACTERIA.
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Proteins found in any species of bacterium.
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).
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
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 process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
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).
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.
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.
Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.
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.
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.
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.
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.
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)
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 intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Genotypic differences observed among individuals in a population.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
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.
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 biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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).
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The sum of the weight of all the atoms in a molecule.
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The functional hereditary units of VIRUSES.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)
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.
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.
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.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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).
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.
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).
Ribonucleic acid that makes up the genetic material of viruses.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
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.
Proteins prepared by recombinant DNA technology.
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.
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
Proteins found in any species of virus.
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.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
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 phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
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.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The functional hereditary units of FUNGI.
A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
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.
Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.
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)
A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
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.
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The genetic complement of a BACTERIA as represented in its DNA.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
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.
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.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
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.
Sequential operating programs and data which instruct the functioning of a digital computer.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Transport proteins that carry specific substances in the blood or across cell membranes.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.
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 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.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.
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.
Deoxyribonucleic acid that makes up the genetic material of plants.
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.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Proteins isolated from the outer membrane of Gram-negative bacteria.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Diseases of plants.
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.
The sequential location of genes on a chromosome.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
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 genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The rate dynamics in chemical or physical systems.
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.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA 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 DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
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.
Procedures for identifying types and strains of fungi.
A country spanning from central Asia to the Pacific Ocean.
Proteins that form the CAPSID of VIRUSES.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
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)
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Proteins found in any species of fungus.
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.
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.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
Proteins obtained from ESCHERICHIA COLI.
Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).
A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.
A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or 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.
Nucleic acid sequences involved in regulating the expression of genes.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
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.
Life or metabolic reactions occurring in an environment containing oxygen.
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.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
A genus of asporogenous bacteria that is widely distributed in nature. Its organisms appear as straight to slightly curved rods and are known to be human and animal parasites and pathogens.
The functional hereditary units of PLANTS.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
Deoxyribonucleic acid that makes up the genetic material of protozoa.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
A ubiquitous sodium salt that is commonly used to season food.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Actual loss of portion of a chromosome.
Refuse liquid or waste matter carried off by sewers.
Deoxyribonucleic acid that makes up the genetic material of archaea.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
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.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.
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.

Structural characterization of the N-linked oligosaccharides in bile salt-stimulated lipase originated from human breast milk. (1/3405)

The detailed structures of N- glycans derived from bile salt-stimulated lipase (BSSL) found in human milk were determined by combining exoglycosidase digestion with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The N- glycan structures were conclusively determined in terms of complexity and degree of fucosylation. Ion-exchange chromatography with pulsed amperometric detection, together with mass-spectral analysis of the esterified N- glycans, indicated the presence of monosialylated structures. The molecular mass profile of esterified N- glycans present in BSSL further permitted the more detailed studies through collision-induced dissociation (CID) and sequential exoglycosidase cleavages. The N- glycan structures were elucidated to be complex/dibranched, fucosylated/complex/dibranched, monosialylated/complex/dibranched, and monosialylated/fucosylated/dibranched entities.  (+info)

Alternative splicing of transcripts encoding the alpha- and beta-subunits of mouse glucosidase II in T lymphocytes. (2/3405)

Glucosidase II is a processing enzyme of the endoplasmic reticulum that functions to hydrolyze two glucose residues in immature N -linked oligosaccharides attached to newly synthesized polypeptides. We previously reported the cDNA cloning of the alpha- and beta-subunits of mouse glucosidase II from T cells following copurification of these proteins with the highly glycosylated transmembrane protein-tyrosine phosphatase CD45. Subsequent examination of additional cDNA clones, coupled with partial genomic DNA sequencing, has revealed that both subunits are encoded by gene products that undergo alternative splicing in T lymphocytes. The catalytic alpha-subunit possesses two variably expressed segments, box Alpha1, consisting of 22 amino acids located proximal to the amino-terminus, and box Alpha2, composed of 9 amino acids situated between the amino-terminus and the putative catalytic site in the central region of the molecule. Box Beta1, a variably expressed 7 amino acid segment in the beta-subunit of glucosidase II, is located immediately downstream of an acidic stretch near the carboxyl-terminus. Screening of reverse transcribed RNA by polymerase chain reaction confirms the variable inclusion of each of these segments in transcripts obtained from a panel of T-lymphocyte cell lines. Thus, distinct isoforms of glucosidase II exist that may perform specialized functions.  (+info)

A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. (3/3405)

A novel human complex that can either repress activator-dependent transcription mediated by PC4, or, at limiting TFIIH, act synergistically with PC4 to enhance activator-dependent transcription has been purified. This complex contains homologs of a subset of yeast mediator/holoenzyme components (including SRB7, SRB10, SRB11, MED6, and RGR1), homologs of other yeast transcriptional regulatory factors (SOH1 and NUT2), and, significantly, some components (TRAP220, TRAP170/hRGR1, and TRAP100) of a human thyroid hormone receptor-associated coactivator complex. The complex shows direct activator interactions but, unlike yeast mediator, can act independently of the RNA polymerase II CTD. These findings demonstrate both positive and negative functional capabilities for the human complex, emphasize novel (CTD-independent) regulatory mechanisms, and link the complex to other human coactivator complexes.  (+info)

Structure of cag pathogenicity island in Japanese Helicobacter pylori isolates. (4/3405)

BACKGROUND: cag pathogenicity island (PAI) is reported to be a major virulence factor of Helicobacter pylori. AIM: To characterise cagA and the cag PAI in Japanese H pylori strains. METHODS: H pylori isolates from Japanese patients were evaluated for CagA by immunoblot, for cagA transcription by northern blot, and for cagA and 13 other cag PAI genes by Southern blot. cagA negative strains from Western countries were also studied. Induction of interleukin-8 secretion from gastric epithelial cells was also investigated. RESULTS: All Japanese strains retained cagA. Fifty nine of 63 (94%) strains had all the cag PAI genes. In the remaining four, cag PAI was partially deleted, lacking cagA transcripts and not producing CagA protein. Details of the PAI of these strains were checked; three lacked cagB to cagQ (cagI) and continuously cagS to cag13 (cagII), and the remaining one lacked cagB to cag8. Western cagA negative strains completely lacked cag PAI including cagA. Nucleotide sequence analysis in one strain in which the cag PAI was partially deleted showed that the partial deletion contained 25 kb of cag PAI and the cagA promoter. Interleukin-8 induction was lower with the cag PAI partial deletion strains than with the intact ones. All Japanese cag PAI deleted strains were derived from patients with non-ulcer dyspepsia, whereas 41 of 59 (70%) CagA-producing strains were from patients with peptic ulcers or gastric cancer (p<0.05). CONCLUSIONS: Most Japanese H pylori strains had the intact cag PAI. However, some lacked most of the cag PAI in spite of the presence of cagA. Thus the presence of the cagA gene is not an invariable marker of cag PAI related virulence in Japanese strains.  (+info)

Biased JH usage in plasma cell immunoglobulin gene sequences from colonic mucosa in ulcerative colitis but not in Crohn's disease. (5/3405)

BACKGROUND: Ulcerative colitis is an inflammatory disease of the colonic and rectal mucosa. Autoantibodies have been observed in ulcerative colitis which may have a role in the pathogenesis of the disease. Evidence also suggests that there is an hereditary predisposition towards the disease, although no individual genes have been identified. AIMS: This is a pilot study of immunoglobulin heavy chain genes (IgH) in ulcerative colitis to determine whether they have any particular genetic characteristics which may lead to a better understanding of the disease aetiology. SUBJECTS: Colonic or rectal tissue was obtained from five children with ulcerative colitis. Tissue was also obtained from five children with Crohn's disease and five children who did not have inflammatory bowel disease as controls. METHODS: B cells and IgD+ B cells were identified by immunohistochemistry on frozen sections. Areas of lamina propria containing plasma cells, and areas of IgD+ B cells were microdissected. The immunoglobulin genes were PCR amplified, cloned, and sequenced. Sequences were analysed for content of somatic mutations and composition of heavy chain. RESULTS: An increase in the use of JH6 and DXP'1, and a decrease in the use of JH4, gene segments in immunoglobulin genes from lamina propria plasma cells, and from virgin IgD+ B cells, was found in patients with ulcerative colitis. These biases were not present in the control groups. CONCLUSIONS: There is a fundamental difference in the immunoglobulin genes from patients with ulcerative colitis. Whether this is caused by a difference in content of immunoglobulin gene segments in the germline or a difference in the recombination mechanism is not known.  (+info)

The origin and evolution of green algal and plant actins. (6/3405)

The Viridiplantae are subdivided into two groups: the Chlorophyta, which includes the Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Prasinophyceae; and the Streptophyta, which includes the Charophyceae and all land plants. Within the Streptophyta, the actin genes of the angiosperms diverge nearly simultaneously from each other before the separation of monocots and dicots. Previous evolutionary analyses have provided limited insights into the gene duplications that have produced these complex gene families. We address the origin and diversification of land plant actin genes by studying the phylogeny of actins within the green algae, ferns, and fern allies. Partial genomic sequences or cDNAs encoding actin were characterized from Cosmarium botrytis (Zygnematales), Selaginella apoda (Selaginellales), Anemia phyllitidis (Polypodiales), and Psilotum triquetrum (Psilotales). Selaginella contains at least two actin genes. One sequence (Ac2) diverges within a group of fern sequences that also includes the Psilotum Ac1 actin gene and one gymnosperm sequence (Cycas revoluta Cyc3). This clade is positioned outside of the angiosperm actin gene radiation. The second Selaginella sequence (Ac1) is the sister to all remaining land plant actin sequences, although the internal branches in this portion of the tree are very short. Use of complete actin-coding regions in phylogenetic analyses provides support for the separation of angiosperm actins into two classes. N-terminal "signature" sequence analyses support these groupings. One class (VEG) includes actin genes that are often expressed in vegetative structures. The second class (REP) includes actin genes that trace their ancestry within the vegetative actins and contains members that are largely expressed in reproductive structures. Analysis of intron positions within actin genes shows that sequences from both Selaginella and Cosmarium contain the conserved 20-3, 152-1, and 356-3 introns found in many members of the Streptophyta. In addition, the Cosmarium actin gene contains a novel intron at position 76-1.  (+info)

Cell-specific peptide binding by human neutrophils. (7/3405)

Analysis of peptide binding to human neutrophils (PMN) using phage display techniques has revealed cell-specific motifs reactive with the PMN surface. Phage libraries displaying either linear 9-mer or cyclic 10-mer and 6-mer peptides were incubated with normal human neutrophils followed by elution of bound phage with low pH (pH 2.2) and non-ionic detergent. Three rounds of selection generated several related peptide sequences that bound with high avidity to PMN. Using the linear 9-mer library, PMN-binding phage expressed peptides with the motif (G/A)PNLTGRW. The binding of phage bearing this motif was highly specific since no binding was observed on lymphocytes, fibroblasts, epithelial, or endothelial cells. Functional assays revealed that phage bearing the sequence FGPNLTGRW induced a pertussis toxin-sensitive increase in PMN cytosolic calcium analogous to that observed with Galphai coupled receptors. Other prominent motifs identified included phage bearing the consensus DLXTSK(M/L)X(V/I/L), where X represents a non-conserved position. Phage with this motif bound exclusively to a sub population of human PMN that comprised approximately 50% of the total and did not elicit a calcium response. The binding of such phage to PMN was prevented by co-incubation with competing peptides displaying identical or similar sequences (IC50 range from 0.6 micromol/L to 50 micromol/L for DLXTSK and GPNLTG, respectively). We speculate that these techniques will be useful in identifying functional cell-specific binding motifs and contribute to the development of new therapeutic and diagnostic strategies in human disease.  (+info)

Isolation and characterization of a human homologue of the latrophilin gene from a region of 1p31.1 implicated in breast cancer. (8/3405)

We have identified a region of chromosome 1p31.1 that shows high frequency loss of heterozygosity (LOH) in human breast cancer. This region forms part of a 7 Mb YAC/BAC contig. In order to identify candidate sequences, mutation of which might contribute to the development of disease, we have carried out mapping studies of ESTs localized to 1p31.1. This analysis, coupled with library screening and a modified 5' RACE-PCR strategy, resulted in the identification and characterization of a novel gene (LPHH1) which is located adjacent to the smallest region of overlapping loss (SRO) seen in tumours. The 4209 bp open reading frame of the 7 kb LPHH1 transcript encodes a peptide which shows approximately 65% identity to rat latrophilin, a G-coupled, seven span transmembrane protein, which binds alpha-latrotoxin. In the human sequence, whilst conservation of the transmembrane domain is high, the intra- and extracellular domains show two regions of variable structure, which are presumably generated by alternative splicing. Surprisingly, while expression of the rat gene is tightly restricted to neurological and perhaps some endocrine cells, the human sequence appears to be expressed very widely in all normal tissues tested. Northern and RT-PCR analysis of a panel of tumour cell lines showed that LPHH1 expression was variable, apparently elevated in some lines and absent or markedly reduced in others. Furthermore, characterization of the range of transcripts encoded in a breast tumour cell line, compared to normal breast, suggested that gene product variability was higher in the tumour.  (+info)

This page will contain a bunch ofuse-cases which will drivedevelopment for BioJava 3. Please add them below - Where possible pleasefollow the template.
Returns the profile future stored at this node, but does not force the calculation, yet. This allows alignment tasks for the entire tree to be queued in a post-order traversal before concurrent execution ...
Sequence comparison by alignment is a fundamental tool of molecular biology. In this paper we show how a number of sequence comparison tasks, including the detection of unique genomic regions, can be accomplished efficiently without an alignment step. Our procedure for nucleotide sequence comparison is based on shortest unique substrings. These are substrings which occur only once within the sequence or set of sequences analysed and which cannot be further reduced in length without losing the property of uniqueness. Such substrings can be detected using generalized suffix trees. We find that the shortest unique substrings in Caenorhabditis elegans, human and mouse are no longer than 11 bp in the autosomes of these organisms. In mouse and human these unique substrings are significantly clustered in upstream regions of known genes. Moreover, the probability of finding such short unique substrings in the genomes of human or mouse by chance is extremely small. We derive an analytical expression for the null
BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D str
Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, room 007, in Lyngby ...
Friday, September 4. Psalm 31: The correct sense of Psalm 31 (Greek and Latin 30) is indicated in verse 5: Into Your hand I commend my spirit. This verse, according to Luke 23:46, was the final prayer of our Lord from the Cross, and I take it to indicate the proper voice of this whole psalm. It is the prayer of Jesus, the author and finisher of our faith, who for the joy that was set before Him endured the cross, despising the shame (Heb. 12:2), speaking to His Father in the context of His sufferings and death. This psalm is part of His prayer of faith.. In making this psalm our own, we Christians are subsumed into the voice and prayer of Christ. We partake of His own relationship to the Father. No one, after all, knows the Father except the Son and the one to whom the Son wills to reveal Him (Matt. 11:27). Our only access to God is through Christ and the mediation of His atoning blood. Our incorporation into Christ is the foundation of all our prayer. Only in Christ do we call God our ...
Over the last ten years the amount of biological sequence data available to researchers has increased by several orders of magnitude, and complete genome sequences (nearly nonexistent ten years ago) have become commonplace. Some techniques involved in analyzing nucleotide and amino acid sequences (e.g. BLAST) have become so commonly used in molecular biology that their names have become verbs. This introductory course is aimed at biologists with little or no previous experience, but also at those users who wish to know more about the methods underlying computational sequence analysis tools. Learn how to use the tools at the European Bioinformatics Institute (EBI/EMBL) to find out more about your nucleotide and protein sequences. You will be guided through a series of exercises using sample fragments of sequence. To gain more information about these sequences, you will use a variety of tools to compare the sequences to databases to analyse them ...
Over the last ten years the amount of biological sequence data available to researchers has increased by several orders of magnitude, and complete genome sequences (nearly nonexistent ten years ago) have become commonplace. Some techniques involved in analyzing nucleotide and amino acid sequences (e.g. BLAST) have become so commonly used in molecular biology that their names have become verbs. This introductory course is aimed at biologists with little or no previous experience, but also at those users who wish to know more about the methods underlying computational sequence analysis tools. Learn how to use the tools at the European Bioinformatics Institute (EBI/EMBL) to find out more about your nucleotide and protein sequences. You will be guided through a series of exercises using sample fragments of sequence. To gain more information about these sequences, you will use a variety of tools to compare the sequences to databases to analyse them ...
For #4 you probably would need to create a custom script, because I do not think this is supported by those tools (this feature would probably need to be very flexible and would need to allow substrings of custom length, not only length 2 substrings ...
Suffix arrays and their variants are used widely for representing genomes in search applications. Enhanced suffix arrays (ESAs) provide fast search speed, but require large auxiliary data structures for storing longest common prefix and child interval information. We explore techniques for compressing ESAs to accelerate genomic search and reduce memory requirements. We evaluate various bitpacking techniques that store integers in fewer than 32 bits each, as well as bytecoding methods that reserve a single byte per integer whenever possible. Our results on the fly, chicken, and human genomes show that bytecoding with an exception guide array is the fastest method for retrieving auxiliary information. Genomic searching can be further accelerated using a data structure called a discriminating character array, which reduces memory accesses to the suffix array and the genome string. Finally, integrating storage of the auxiliary and discriminating character arrays further speeds up genomic search. The
The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show that i) the way how we search for the right interval boundary impacts significantly the overall search speed, ii) a B-tree data layout easily wins over the standard one, iii) the well-known idea of a lookup table for the prefixes of the suffixes can be refined with using compression, iv) caching prefixes of the suffixes in a helper array can pose another practical space-time tradeoff.
One example I have of this took place just this past season. A freshmen and 1st year wrestler was having a difficult time. He was not wrestling much, and when he did get a chance, he lost quickly. He was looking dejected and I took a moment to speak with him. I asked him if he remembered his first week of practices, how he could not do the push-ups, keep up on the run, and how sore he was the day after practice. He said yes, and then I reminded him how today he was doing the push-ups, and keeping up on the runs. I let him know he had already lost almost 20 pounds, while getting stronger. As a smile started to creep across his face, I saw that he got it. He got the idea of the long haul of work paying off, over time. He could see the progress and make the link to his hard work all season. He liked it.. His improvement over time was not only limited to his physicality. He has opened up more among his peer group. He is walking taller, smiles more quickly, and is improving academically with much ...
A set of words of a natural language is grouped by automatically obtaining suffix relation data that indicate a relation value for each of a set of relationships between suffixes that occur in the natural language, and, then, by automatically clustering the words in the set using the relation values from the suffix relation data, to obtain group data indicating groups of words. Two or more words in a group have suffixes as in one of the relationships and, preceding the suffixes, equivalent substrings. The relationships can be pairwise relationships, and the relation value can indicate the number of occurrences of a suffix pair. The suffix relation data can be obtained using an inflectional lexicon. Complete link clustering can be used.
SADI is a suite of Stata tools for sequence analysis, with a particular focus on holistic comparisons of sequences using measures such as optimal matching distance. It provides a number of distance measures, including • Optimal matching distance • Hamming distance • Dynamic Hamming distance • Elzingas combinatorial X/t measure and • TWED, a time-warping distance measure. It provides a number of utilities for graphing sequence-related data, for summarising sequences, and for handling sequences in general. The main alternatives to SADI are the Stata SQ package (Brzinsky-Fay, Kohler&Luniak, 2006), and the R package TraMineR (Gabadinho, Ritschard, Studer & Müller, 2009). SADI provides some tools that are not in SQ, and is much faster for some important functions. TraMineR is pretty attractive for those working in R, but SADI makes it possible to do a lot in a Stata environment, and has distance measures that are not in TraMineR. Since some of the distance measures are relatively ...
το κείμενο με τίτλο Neural Networks for Biological Sequence Classification σχετίζετε με Δίκτυα και Επικοινωνίες
Nitrile Phenolic Thermosetting Adhesive Film RFA-142 is Black in color and is chemically resistant to Brake fluid, oils, water. RFA-142 is recommended for bonding Bonding friction material to metal.
A Computer Science portal for geeks. It contains well written, well thought and well explained computer science and programming articles, quizzes and practice/competitive programming/company interview Questions.
N a(n) is the lexically first sequence of distinct nonzero integers such that if S(n) is the string formed from the digits of a(1)a(2)...a(n), then dividing S(n) into substrings with lengths equal to the successive digits of S(n) (treating 0 as 10) results in substrings beginning with the successive digits of Pi (A000796 ...
Does anyone know of a reliable organization or company where I can send my protein for N-terminal amino acid sequencing? Michael R. King (king1 at students.uiuc.edu ...
Hi guys, Back from a sunny and warm long weekend, let me continue our discussion on framework design and implementation based on Koens input. Let me start by proposing an idea which again is derived from the BioJava framework. I think also in this respect they must have had a similar discussion as we are having here, and I see there solution to the problem as a very nice one. First an explanation of the idea, then my thoughts in this light as a reply to the things brought up. Basically we have two options: either go for a string based solution (as sequences are kind of long strings in the end), or go for a specific sequence class approach. As outlined in the link above, the string based approach has some clear disadvantages: 1 One would constantly need validation of strings as they allow non existing characters. I use strings in my programs to store sequences (I bet everyone does) and I constantly strip foreign characters upon editing, copying, dragging etc, in fact thats how I call my ...
Streaming Algorithms for Biological Sequence Alignment on GPUs | Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang M. Wittig | Biology, Sequence alignment
Classification of Biological Sequences: 10.4018/978-1-61350-056-9.ch007: The rapid progress of computational biology, biotechnology, and bioinformatics in the last two decades has led to the accumulation of tremendous amounts of
In this paper, we investigate the chaotic behavior of the biological sequences among the different species. Throughout this work, we have characterized the biological sequences according to their moment invariant, correlation dimension, and largest Lyapunov exponent estimates. We have applied our model to a number of human and mouse genomes encoded into a set of integers (time series) using a plain table mapping scheme. Our results indicate that the nonlinear dynamical characteristics have yielded significant differences between the sequences of the different species. That is, we have been able to classify the different genome sequences according to their chaotic parameters estimates. On the other hand, through our investigation we have found that the use of the chaotic modeling of the biological sequences could open new frontiers in the sequence similarity search ...
Primary amino acid sequencing is performed on your biopharmaceutical to determine the correct positions of each and every amino acid.
A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
Sequence analysis of Hd1 in lf1132 and wild type.A: The sequence differences between wild type and lf1132. The black triangle represents insertion; vertical lin
Sequence analysis at the borders of the amplified XylA-locus, and verification of the presence of circular or tandem repeats.(A) Illumina sequence reads mapped
-ee suffix a. One that receives or benefits from a specified action: addressee. b. One that possesses a specified thing: mortgagee. One that performs a
Chang, E., et al. N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis. Journal of Biomolecular Technology. 27(2). 07/03/2016.. ...
With SGS N-terminal Sequencing, clients receive an accurate, competitive and expert service that helps reduce the time it takes to get a drug to market. Find out today how we can help you sequence proteins from their N-terminus.
Mouse Genome Sequencing Consortium) (December 2002). "Initial sequencing and comparative analysis of the mouse genome". Nature ... Bambara R, Wu R (June 1975). "DNA sequence analysis. Terminal sequences of bacteriophage phi80". The Journal of Biological ... Barrell BG, Weith HL, Donelson JE, Robertson HD (March 1975). "Sequence analysis of the ribosome-protected bacteriophase ... Feldmann H (July 1967). "[Sequence analysis of oliogonucleotides by means of micrococcal nuclease]". European Journal of ...
Bakhtin provided concepts such as dialogism from which come techniques such as Dialogical Sequence Analysis. This is a ... Original works published in 1934, 1960). Leiman, M. (2004). Dialogical sequence analysis. In: H. J. M. Hermans & G. Dimaggio ( ... A review of CAT looking back over the 30 years to its beginnings contains a meta-analysis of 11 outcome studies of CAT. The ... In addition to the procedural sequence model, a second distinguishing feature of CAT is the use of reciprocal roles (RRs). ...
Missing sequence identification. Statistical analysis. Calculations. Duplicate transaction identification. Pivot table creation ... in sequences) for a specific field. For example, finding a broken sequence in an invoice number sequence. Sort field: Specifies ... Age analysis: Specifies whether the product supports making age analysis (stratification by date). Benford's law: Specifies ... Generally, however, it is used to refer to any data extraction and analysis software. This would include programs such as data ...
Huang, T. S. (1981). Image Sequence Analysis. Springer Science & Business Media. p. 29. ISBN 9783642870378. Stanković, Radomir ... One example is Motion JPEG, which is simply a sequence of individually JPEG-compressed images. This approach is quick and ... Roese, John A.; Robinson, Guner S. (30 October 1975). "Combined Spatial And Temporal Coding Of Digital Image Sequences". ... Interframe compression complicates editing of an encoded video sequence. One subclass of relatively simple video coding formats ...
Huang, T. S. (1981). Image Sequence Analysis. Springer Science & Business Media. p. 29. ISBN 9783642870378. Chen, Wen-Hsiung; ... There are several advantages of global motion compensation: It models the dominant motion usually found in video sequences with ... Roese, John A.; Robinson, Guner S. (30 October 1975). "Combined Spatial And Temporal Coding Of Digital Image Sequences". ... B frames are more complex because the image sequence must be transmitted and stored out of order so that the future frame is ...
On the basis of Mikhail Bakhtin's theory of utterances, Leiman devised a dialogical sequence analysis. This method starts from ... Leiman, M. (2004). Dialogical sequence analysis. In: H. J. M. Hermans & G. Dimaggio (eds.), The dialogical self in ... On the basis of the results of the quantitative analysis, some positions can be selected, by the client or assessor, for closer ... The simplest approach, however, is to perform a standard principal component analysis (PCA). To obtain a bi-plot, a PCA is once ...
Purification and sequence analysis". J. Biol. Chem. 262 (12): 5808-11. PMID 3571235. Dahr W, Beyreuther K, Moulds J, Unger P ( ... It was first sequenced in 1987 the peptide sequence of 72 amino acids having been determined earlier that year. The gene has 97 ... The transition site from homologous to nonhomologous sequences can be localized within Alu repeat sequences. There are ~80000 ... There is a signal sequence of 19 amino acid residues. The leader peptide differs by one amino acid and the next 26 amino acids ...
Protein sequence analysis & classification. InterPro. Retrieved 1 May 2018. "Annotation and Analysis". ElDorado. Genomatix. ... The peptide sequence lacks a signal sequence either at the N-terminus or internally. No transmembrane domains have been ... This sequence is partially complementary to the human gene PCNX1. A total of 20 transcript variants of FAM208b, including one ... Protein FAM208B (family with sequence similarity 208 member b) is a protein that in humans is encoded by the FAM208B gene. The ...
I. Nucleotide sequence analysis". J. Mol. Biol. 131 (3): 573-592. doi:10.1016/0022-2836(79)90008-1. PMID 390161. Ikemura, ... In E. coli the spf gene is flanked by polA (upstream) and yihA (downstream). A CRP binding sequence and -10 and -35 promoter ... Bækkedal and Haugen made a Spot42 consensus secondary structure based on all known "spf" sequences at the time (2015) and found ... Beisel and Storz demonstrated with microarray analysis and reporter fusions that Spot 42 plays a broader role in metabolism by ...
Analysis of the reaction sequence". The Journal of Biological Chemistry. 266 (10): 6324-8. PMID 2007585. "EC 2.10.1". School of ... Their analysis showed that this reversible reaction could be applied to other tissues. This assertion was validated by Rudolf ... These efforts are focused on sequencing the subunits of the rubber transferase enzyme complex in order to transfect these genes ... Dobrowolski SF, Banas RA, Suzow JG, Berkley M, Naylor EW (Feb 2003). "Analysis of common mutations in the galactose-1-phosphate ...
An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition". Bioinformatics for DNA Sequence ... The mRNA sequence is determined by the sequence of genomic DNA.[4] In such context, the standard genetic code is referred to as ... the sequence AUG-read as methionine-can serve as a start codon and, along with sequences such as an initiation factor, ... A codon table can be used to translate a genetic code into a sequence of amino acids.[1][2] The standard genetic code is ...
Chimpanzee Sequencing; Analysis Consortium (September 2005). "Initial sequence of the chimpanzee genome and comparison with the ... in an article produced by the Chimpanzee Sequencing and Analysis Consortium.[73] ... Evidence from fossils and DNA sequencing shows both species of the genus Pan are the sister taxon to the modern human lineage. ... The DNA sequence differences between humans and chimpanzees is about 35 million single-nucleotide changes, five million ...
"NetPhos 2.0 Server". Center for Biological Sequence Analysis. Retrieved 13 May 2013. "SUMOsp 2.0 - SUMOylation Site Prediction ... According to an analysis of the secondary protein structure, TTC39B is most likely to be expressed in the endoplasmic reticulum ...
Center for Biological Sequence Analysis. Miao, Y.; Cui, L.; Chen, Z.; Zhang, L (2016). "Gene expression profiling of DMU-212- ... "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences. 89 (6 ... Co-expression analyses have found that TMEM217 was up-regulated in response to mechanical stretch in dermal fibroblast cells ... No known function has been attributed to TMEM217, however a co-expression analysis in dermal fibroblasts has predicted the ...
Analysis of the reaction sequence". J. Biol. Chem. 266 (10): 6324-8. PMID 2007585. Biology portal v t e. ...
Center of Biological Sequence Analysis. Retrieved 9 May 2015. "NetPhosK 1.0 Server". NetPhosK 1.0 Server. Center of Biological ... Sequence Analysis. Retrieved 9 May 2015. "NetAcet 1.0 Server". NetAcet 1.0 Server. Center of Biological Sequence Analysis. ... TMEM251 has a multitude of mutations in its 5'UTR, coding sequence, and 3'UTR. The majority of the mutations observed are ... Both consists of two exons that include the entire coding sequence for the TMEM251 protein. Figure 1: Chromosome 14 overview. ...
... and Proteomics at MIT Mount D (2000). Bioinformatics, Sequence and Genome Analysis. Cold Spring Harbor ... refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, ... Beginning in the 1980s, databases of genome sequences began to be recorded, but this presented new challenges in the form of ... Later, the BLAST algorithm was developed for performing fast, optimized searches of gene sequence databases. BLAST and its ...
An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition". Bioinformatics for DNA Sequence ... The mRNA sequence is determined by the sequence of genomic DNA. In such context, the standard genetic code is referred to as ... In the standard code, the sequence AUG-read as methionine-can serve as a start codon and, along with sequences such as an ... Three sequences, UAG, UGA, and UAA, known as stop codons, do not code for an amino acid but instead signal the release of the ...
July 2019). "The EMBL-EBI search and sequence analysis tools APIs in 2019". Nucleic Acids Research. 47 (W1): W636-W641. doi: ... Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... June 2008). "Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences". Cell. 133 (7 ... the 18 zf-C2H2 binding domains are predicted to bind to the DNA sequence shown in the sequence logo (Figure 7-9). A mutation ...
2012). "Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing". Nature. 487 (7407): 375-9. ... Magnus Manske on Twitter Alastair Kerr (21 June 2011). "Desktop Sequence Analysis: software review". Bioinformatics Knowledge ... Manske, H. M.; Kwiatkowski, D. P. (2009). "Look Seq: A browser-based viewer for deep sequencing data". Genome Research. 19 (11 ... which minimizes errors in sequencing. As a student, Manske was one of the most active contributors to the Nupedia project, ...
Protein Sequence and Data Analysis. Vol. 15(1): 31 - 32 (1992) The following are a few of the contributions made to textbooks ... Journal of Protein Sequence and Data Analysis Vol.. 11: 410 - 412 (1993) Characterization of two Platelet Aggregation Inhibitor ... 374: 363 - 366 (1995) The complete sequence of human lens γs Crystallins. J B Smith, Z Yang, P. Lin, Zafar H. Zaidi, A. Abbasi ... He organized six international symposia and workshops on Protein structure function and was a coordinator of the DNA Sequence ...
... an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts". Bioinformatics ... Shin SW, Kim SM (15 Jan 2005). "A novel complexity measure for comparative analysis of protein sequences from complete genomes ... Claverie JM, States D (June 1993). "Information enhancement methods for large scale sequence analysis". Computers Chem. 17 (2 ... Wootton JC, Federhen S (June 2003). "Statistics of local complexity in amino acid sequences and sequence databases". Computers ...
"NetOGlyc". Center for Biological Sequence Analysis. "NetNES". Center for Biological Sequence Analysis. "SAPS". SDSC Biology ... The primarily used sequence in humans is C9orf84 Isoform 1. This isoform is 1444 aa long, contains 26 exons, has a predicted ... "A comprehensive functional analysis of tissue specificity of human gene expression". BMC Biology. 6: 49. doi:10.1186/1741-7007- ...
Comparative sequence analysis indicates features typical for mt-tmRNAs. Most conserved is the primary sequence of the amino ... Zwieb C, Wower I, Wower J (May 1999). "Comparative sequence analysis of tmRNA". Nucleic Acids Research. 27 (10): 2063-71. doi: ... Eddy SR, Durbin R (June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-88. doi: ... The complete E. coli tmRNA secondary structure was elucidated by comparative sequence analysis and structural probing. Watson- ...
Padmanabhan, R.; Wu, Ray (1972). "Use of oligonucleotides of defined sequences as primers in DNA sequence analysis". ... Wu, Ray (April 19, 1972). "Nucleotide Sequence Analysis of DNA". Nature. 236 (68): 198-200. doi:10.1038/newbio236198a0. PMID ... Plant genetics pioneer Ray Wu invented the first method for sequencing DNA, considered a major breakthrough in genetics as it ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the ... Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation ... Johansen MB, Kiemer L, Brunak S (September 2006). "Analysis and prediction of mammalian protein glycation". Glycobiology. 16 (9 ...
Robson, B. (1974). "Analysis of the Code Relating Sequence to Conformation in Globular Proteins: Theory and Application of ... The method is therefore essentially Bayesian in its analysis. The GOR method analyzes sequences to predict alpha helix, beta ... ISBN 0-87969-712-1. Robson, B.; Pain, R. H. (1971). "Analysis of the Code Relating Sequence to Conformation in Globular ... Mount, D. M. (2004). Bioinformatics: Sequence and Genome Analysis. 2. Cold Spring Harbor Laboratory Press. ...
Analysis sequence and CALIFA dataproducts". Revista Mexicana de Astronomía y Astrofísica. 52: 171-220. arXiv:1602.01830. ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... The predicted promoter sequence overlaps with the 5'UTR and coding sequence of Pericentrin (PCNT) on the plus strand of ... DNA microarray analysis from various experiments showed variable C21orf58 expression in unique physiological conditions. An ... Garnier J, Osguthorpe DJ, Robson B (March 1978). "Analysis of the accuracy and implications of simple methods for predicting ...
Analysis of the reaction sequence". J. Biol. Chem. 266 (10): 6324-8. PMID 2007585. Biology portal. ...
And each case seems to present a new low in terms of the depth and quality of analysis." She sees a common thread in these ... So they wanted to focus on genetic fragments containing paternally inherited sequences the mother did not share, but had ... Noonan concedes that the type of analysis described in Flook "may make sense in claims to" electromechanical inventions such as ... The overbreadth of the Federal Circuit's analysis threatens diagnostic methods across the board. If a method of detecting a ...
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human ... International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.. Nature. 2001, 409 (6822 ... Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome.. Nature. 2002, 420 (6915 ... Genome sequence, comparative analysis and haplotype structure of the domestic dog.. Nature. 2005, 438 (7069): 803-19. PMID ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... 2002). "Complete mutation analysis panel of the 39 human HOX genes". Teratology. 65 (2): 50-62. doi:10.1002/tera.10009. PMID ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ...
Genetic analysis indicates that there has been an unbroken genetic continuity[clarification needed] of the inhabitants over the ... "Record of the Vistula ice lobe advances in the Late Weichselian glacial sequence in north-central Poland". Quaternary ...
Mendham, J.; Denney, R. C.; Barnes, J. D.; Thomas, M. J. K. (2000), Vogel's Quantitative Chemical Analysis (6th ed.), New York ... Ozonolysis, and related dihydroxylation/oxidative sequences, cleave alkenes to give aldehydes or ketones, depending on alkene ...
The sequence has been published on the website OpenAshDieBack and offers clues to how the fungus infects trees. The study has ... Genetic analysis of the fungus Lambertella albida which grows harmlessly on petioles of the Manchurian ash (Fraxinus ... Teams from The Sainsbury Laboratory (TSL) and the John Innes Centre in Norwich sequenced the genome of the fungus in December ... In December 2016, writing in Nature Dr Richard Buggs reported that the common ash (Fraxinus excelsior)had been sequenced for ...
Analysis of variance[edit]. The simplest method for QTL mapping is analysis of variance (ANOVA, sometimes called "marker ... Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this ... This can be done using BLAST, an online tool that allows users to enter a primary sequence and search for similar sequences ... INTERSNP - a software for genome-wide interaction analysis (GWIA) of case-control SNP data and analysis of quantitative traits ...
... carbohydrate recognition and analysis of the b-prims fold". Protein Science. 8 (1): 13-24. doi:10.1110/ps.8.1.13. PMC 2144112. ... "Km+, a mannose-binding lectin from Artocarpus inegrifolia: amino acid sequence predicted tertiary structure, ...
"The Return on Investment for Ingenuity Pathways Analysis within the Pharmaceutical Value Chain", Zimmerman, Reeve, and Golden, ... Laboratory Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing ... "Ingenuity Preps New NGS Variant Analysis Tool, Signs Translational Oncology Group as Beta Tester". BioInform. GenomeWeb. ... "Ingenuity IPA Software - Pathway Analysis, miRNA, NGS, RNA-Seq, Microarrays, Gene Expression, Biomarkers". Ingenuity Systems. ...
An analysis of mitochondrial DNA sequences published in 2003 confirmed that the black-billed magpie and the yellow-billed ...
The figure has the same harmonic sequence as the earlier offbeat/onbeat example, but rhythmically, the attack-point sequence of ... Gerhard Kubik cited by Agawu, Kofi (2006: 1-46). "Structural Analysis or Cultural Analysis? Comparing Perspectives on the ' ... Mathematical analysis[edit]. In addition to these three branches of theory, clave has in recent years been thoroughly analyzed ... 8 rhythm as a feel, a term usually reserved for those aspects of musical nuance not practically suited for analysis. As used by ...
The recent advances in next-generation sequencing and comparative genomics have enabled the development of robust and reliable ... further analysis showed that neutrophils exposed to dead H. influenzae were more aggressive in attacking S. pneumoniae.[28] ...
1987). "Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA". Nature. 329 (6137): 343-346. doi: ... "Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a ...
... and published his completed analysis in 1794;[3] in 1797, the new oxide was named yttria.[4] In the decades after French ... to this debate on the basis of moving to a 32-column table and consideration of which option results in a continuous sequence ...
Three-dimensional images of tracer concentration within the body are then constructed by computer analysis. In modern PET ... Because the two scans can be performed in immediate sequence during the same session, with the patient not changing position ... 2002). "Brain imaging of 18F-fallypride in normal volunteers: Blood analysis, distribution, test-retest studies, and ... including the use of light pipes and volumetric analysis, have been important in the deployment of PET imaging. In 1961, James ...
Analyses of vein patterns often fall into consideration of the vein orders, primary vein type, secondary vein type (major veins ... There is a regularity in these angles and they follow the numbers in a Fibonacci sequence: 1/2, 2/3, 3/5, 5/8, 8/13, 13/21, 21/ ... A Fractal Analysis Approach to Tune Mechanical Rigidity of Scaffolding Matrix in Thin Films". Advanced Materials Research. 1141 ... "Leaf Vascular Systems in C3 and C4 Grasses: A Two-dimensional Analysis". Annals of Botany. 97 (4): 611-621. doi:10.1093/aob/ ...
Genome-sequencing showed that this outbreak was not related to the 2014-15 West Africa Ebola virus outbreak, but was the same ... "Virological Analysis: no link between Ebola outbreaks in west Africa and Democratic Republic of Congo". World Health ... Genome sequencing suggests that this outbreak, the 11th outbreak since the virus was first discovered in the country in 1976, ... December 1999). "Identification of Ebola virus sequences present as RNA or DNA in organs of terrestrial small mammals of the ...
The analyses of the study show that complications were more likely in patients with pre-operative comorbidities. Patients older ... The CRH test uses recombinant human or bovine-sequence CRH, which is administered via a 100μg intravenous bolus dose. The ...
A sequence of two high-profile studies by a team from the Massachusetts Institute of Technology and the Harvard School of ... "State Medicaid Expansions and Mortality, Revisited: A Cost-Benefit Analysis" (PDF). American Journal of Health Economics. 3 (3 ...
Genetic analysis has shown that certain mallards appear to be closer to their Indo-Pacific relatives while others are related ... The genome of Anas platyrhynchos was sequenced in 2013.[6] ... Mitochondrial DNA data for the D-loop sequence suggests that ...
"Phylogeographic Analysis of the mid-Holocene Mammoth from Qagnax Cave, St. Paul Island, Alaska" (PDF).. ... "Callaway, Ewen (22 September 2011), "First Aboriginal genome sequenced", Nature, Nature News, doi:10.1038/news.2011.551 ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-45. doi:10.1038/ ...
Its existence was first proven in 1962,[4] and first sequenced in 1986-when two Japanese research teams sequenced the ... "Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of ... both very common in chloroplast transit sequences-making up 20-30% of the sequence)[45] are often the amino acids that accept ... Chloroplast transit peptides exhibit huge variation in length and amino acid sequence.[42] They can be from 20-150 amino acids ...
Hilberg's analysis of the steps that led to the destruction of European Jews revealed that it was "an administrative process ... "sequence of steps in a destruction process is thus determined". If a bureaucracy is motivated "to inflict maximum damage upon a ...
... Circuit Analysis - Theory and Solutions to 235 Problems; 2nd Ed; Alfred Gronner; Simon and Schuster; 244 pages; 1970 ... A 3-digit sequence number (or one letter then two digits, for industrial types) follows. With early devices this indicated the ...
"Genome sequence and analysis of a Propionibacterium acnes bacteriophage". Journal of Bacteriology. 189 (11): 4161-7. doi: ... a systematic review and meta-analysis". The British Journal of Dermatology (Systematic Review & Meta-Analysis). 173 (5): 1132- ... "Journal of Zhejiang University Science B (Meta-analysis). 13 (3): 192-202. doi:10.1631/jzus.B1100285. PMC 3296070. PMID ... "Annals of Family Medicine (Systematic Review & Meta-Analysis). 17 (6): 545-553. doi:10.1370/afm.2445. PMC 6846280. PMID ...
2004). "Mass spectrometry analysis of recombinant human ZP3 expressed in glycosylation-deficient CHO cells". Biochemistry. 43 ( ... A variation in the last exon of this gene has previously served as the basis for an additional ZP3 locus; however, sequence and ... The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage ...
"Data analysis slides by Center for International Blood and Marrow Transplant Research". mcw.edu. Archived from the original on ... mismatch as small as a single DNA base pair is significant so perfect matches require knowledge of the exact DNA sequence of ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... 2007). "Proteomic analysis of human very low-density lipoprotein by two-dimensional gel electrophoresis and MALDI-TOF/TOF". ... Kamboh MI, Aston CE, Hamman RF (2000). "DNA sequence variation in human apolipoprotein C4 gene and its effect on plasma lipid ... "Large-scale candidate gene analysis of spontaneous clearance of hepatitis C virus". J. Infect. Dis. 201 (9): 1371-80. doi ...
... a vertex sequence such that each edge goes from an earlier vertex to a later vertex in the sequence.. totally disconnected. ... 2. Power graph analysis is a method for analyzing complex networks by identifying cliques, bicliques, and stars within the ... The degree sequence is the collection of degrees of all vertices, in sorted order from largest to smallest. In a directed graph ... A path may either be a walk (a sequence of vertices and edges, with both endpoints of an edge appearing adjacent to it in the ...
According to Michael Levitt, sequence analysis was born in the period from 1969-1977. In 1969 the analysis of sequences of ... Pair-wise sequence alignment only compares two sequences at a time and multiple sequence alignment compares many sequences. Two ... Machine Clustering Bayesian Network Regression Analysis Sequence mining Alignment-free sequence analysis List of sequence ... In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... Motif-based sequence analysis tools. *PROSITE. Detection of sequence patterns with interfaces at ExPASy (Switzerland). *Smith- ... Sequence Analysis Resources. *BLAST. Basic Local Alignment Tool with interfaces at: *DDBJ (Japan) *EMBL (Germany) *EMBNET ( ... Implementations of FASTA (Pearson and Lipman) sequence alignment method at: *DDBJ (Japan) *EBI (UK) *Georgetown University (USA ...
COMP 571 BIOINFORMATICS: SEQUENCE ANALYSIS. Spring 2017. (Fall 2010 offering,Spring 2016 offering) [Staff] [Discussion Forum] [ ... Sequence alignment: General overview. Slides (full), Slides (handout) 3. Sequence alignment: Scoring schemes. Slides (full), ... "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin et al., Cambridge University Press ... INTENDED AUDIENCE: Anyone interested in learning about algorithms and their use in biological sequence analysis. A solid ...
In quantitative analyses, we analyse nominal and continuous variables, or so we are taught. For example: is a country ... Sequence analysis, originally developed in biology to analyse DNA sequences, is a longitudinal method that allows to analyse ... Aisenbrey & A. E. Fasang (2010). New Life for Old Ideas: The "Second Wave" of Sequence Analysis Bringing the "Course" Back ... In quantitative analyses, we analyse nominal and continuous variables, or so we are taught. For example: is a country ...
... one or more sequences may be misaligned; (iii) the sequences may be contaminated, meaning that some sequences in the alignment ... Highly specific protein sequence motifs for genome analysis. Craig G. Nevill-Manning, Thomas D. Wu, and Douglas L. Brutlag ... The first sequence, however, contains a proline at this position. This may be the result of a sequencing error, a rare mutation ... 1996) GeneQuiz II: Automatic Function Assignment for Genome Sequence Analysis, Pacific Symposium and Biocomputing, 1996 (World ...
Differential expression analysis for sequence count data.. Anders S1, Huber W. ... High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of ... In contrast, the Poisson GLM analysis produced strong enrichments of small P values; this is a reflection of overdispersion in ... The upper row corresponds to an analysis with DESeq (D), the lower row to one based on Poisson GLMs (P). If no true ...
Complete genome sequence and analysis of Wolinella succinogenes. Claudia Baar, Mark Eppinger, Guenter Raddatz, Jörg Simon, ... Complete genome sequence and analysis of Wolinella succinogenes. Claudia Baar, Mark Eppinger, Guenter Raddatz, Jörg Simon, ... Complete genome sequence and analysis of Wolinella succinogenes. Claudia Baar, Mark Eppinger, Guenter Raddatz, Jörg Simon, ... The final sequencing error rate was estimated to be ,0.67 × 10-5 by using the phred/phrap/consed software package (17-20). The ...
This book presents molecular biology knowledge and mathematical theories of frequently-used algorithms in sequence comparison, ...
UGENE - a free and open source DNA and protein sequence analysis tool. The goal of the project is to integrate most of the ... readseq - Reads and writes nucleic/protein sequences in various format * SEALS - SEALS (A System for Easy Analysis of Lots of ... MPSRCH - MPSRCH™ is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha. ... Toucan - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated ...
Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdSgene sequences as... ... Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of ... In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, ... The housekeeping gene sequences were provided from the ongoing sequencing project of B. unamae MTl-641T, B. tuberum STM678T, B ...
Sequence Similarity Search (SSS) is a method of searching sequence databases by using alignment to a query sequence. By ... Compare a sequence with those contained in nucleotide and protein databases using NCBI BLAST. ... assessing how well database and query sequences match one can infer homology and transfer information to the query sequence. ...
Phylogenetic tree of 16S rRNA gene sequences from Iron Mountain community genome sequencing (red) and selected sequences from ... Community-wide analysis of microbial genome sequence signatures.. Dick GJ1, Andersson AF, Baker BJ, Simmons SL, Thomas BC, ... Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional ... Ferroplasma types I/II are not shown due to their near-identical sequences to F. acidarmanus. Sequences for which only partial ...
The latest release of Net-IDs hidden Markov model simulator for biological sequence analysis, HMMpro 2.1, is now available at ...
The technology, called PANGEA (predictive analysis of noncoding genomic enhancer/promoter alterations), could eventually help ... GenomSys Banks on MPEG-G Standard to Make Genome Analysis Mobile. Premium ...
Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep ... Deep Sequencing Data Analysis. Editors. * Noam Shomron Series Title. Methods in Molecular Biology. Series Volume. 1038. ... The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read ... any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, ...
Social sequence analysis is a special application of sequence analysis, a set of methods that were originally designed in ... Brendan Halpins sequence analysis page at the University of Limerick.. *Laurent Lesnards Stata plugin for sequence analysis ... The Sequence Analysis Association (SAA) was founded at the International Symposium on Sequence Analysis and Related Methods, in ... of sequence analysis.[40] Scholars who have made important contributions to social sequence analysis theory, techniques, data ...
... has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence inser- ... merges the contigs of different individuals into high-confidence sequences, anchors the merged sequences into the reference ... Genome analysis PopIns: population-scale detection of novel sequence insertions Cached. * Download Links. * [bioinformatics. ... title = {Genome analysis PopIns: population-scale detection of novel sequence insertions},. year = {}. }. ...
Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. ... Allison, L., Stern, L., Edgoose, T., Dix, T.I.: Sequence complexity for biological sequence analysis. Computers & Chemistry 24 ... web-based software toolkit DNA sequence analysis DNA compression This is a preview of subscription content, log in to check ... Pratas D., Pinho A.J., Garcia S.P. (2012) Exon: A Web-Based Software Toolkit for DNA Sequence Analysis. In: Rocha M., Luscombe ...
Mathematica 7 adds sequence analysis tools that operate on both strings and general lists, and are fully integrated into the ... Mathematica 7 adds industrial-strength state-of-the-art sequence analysis tools. Suitable for bioinformatics, text analysis and ... the sequence analysis tools operate on both strings and general lists, and are fully integrated into the general Mathematica ...
... designing and using gene panels for targeted analysis, and maximizing data analysis accuracy. ... Download this eBook from The Scientist and BD Biosciences to learn about the advantages of targeted single-cell analysis, ... Sequence Analysis. Learn about the advantages of targeted single-cell analysis for designing gene panels and maximizing data ... Next-generation sequencing-based single-cell whole transcriptome amplification analysis techniques can overcome this limitation ...
... you need to know the methodology for your analysis is selected by world-class experts. SGS C-terminal Sequencing is carried out ... As there is no standard approach to confirm the C-terminal sequence, ... Home › Life Sciences › Biopharmaceutical Services › Laboratory Services › Protein and Peptide Analysis › C-Terminal Sequence ... Life Sciences C-Terminal Sequence Analysis. The determination of C-terminal microheterogeneity is crucial to guarantee a high- ...
High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of ... Differential expression analysis for sequence count data Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub ... High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of ...
In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy ... addresses the analysis of communication systems and has been widely applied in molecular biology. ... Information theory applications for biological sequence analysis Brief Bioinform. 2014 May;15(3):376-89. doi: 10.1093/bib/ ... In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy ...
DNA sequence analysis:. The output sequence traces from the sequencer were pretrimmed using PHRED with a quality score of 13 or ... Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, ... 2005). One aim of the present study was to compare SSAP-based diversity analysis with gene-based sequence diversity analysis, ... DNA sequencing:. Sequencing PCR reactions used 0.33 μl Big Dye Terminator v3.1 Cycle Sequencing RR-100 (Perkin-Elmer, Norwalk, ...
... and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses ... and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic ... Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial ... The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including ...
Choke point analysis of the metabolic pathways of Acinetobacter baylyi: A genomics approach to assess potential drug targets ... Vitis vinifera gene expression differential analysis assessing microarrays data pre-processing dynamism by RNA-Seq approach ... Evaluating the computing efficiencies (specificity and sensitivity) of graphics processing unit (GPU)-accelerated DNA sequence ... A computational technique for prediction and visualization of promoter regions in long human genomic sequences ...
DNA/protein sequence analysis.. Read 2 user reviews of Sequence Analysis on MacUpdate. ... Download the latest version of Sequence Analysis for Mac - ... Sequence Analysis is sequence editing, reverse complement, ... Sequence Analysis. Version 2.0.0: Release notes were unavailable when this listing was updated. ... Fetches sequence entries directly from the NCBI via Accession number or GID. Reads most sequence formats. ...
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. The source code for ... The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009. The aligner ... Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short DNA sequences." The speed increase of Bowtie is ... Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat, Cufflinks and ...
  • The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. (wikipedia.org)
  • Expression Analysis (www.ExpressionAnalysis.com) provides whole genome to focused set gene expression and genotyping assays along with DNA sequencings services, sequence enrichment technologies and bioinformatics support. (fiercebiotech.com)
  • The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications. (frontiersin.org)
  • Whole genome sequencing and its clinical relevance are presented particularly in the context of analysis of nucleotide and structural genomic variants in large population studies and in certain patient cohorts. (frontiersin.org)
  • Our laboratory is analyzing a large amount of human genome sequence data (whole genome, exome, and RNA-seq) by using cutting-edge next-generation sequencers and performing highly innovated informatics approach, and is providing basic genome information to clarify the relationship between genetic variations and cancer, human diseases, and drug response. (riken.jp)
  • Whole genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. (riken.jp)
  • Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). (harvard.edu)
  • Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). (harvard.edu)
  • A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species. (illumina.com)
  • Recent advances in microbial whole genome sequencing and metagenome analysis using next generation sequencing play an increasingly important role in the assessment of microbial risks. (bund.de)
  • Whole genome sequencing also offers major benefits for the future characterisation of foodborne disease pathogens. (bund.de)
  • Conventional typing techniques such as serotyping, target gene amplification of specific genes (e.g. toxin genes), antimicrobial resistance gene determination, pulsed-field gel electrophoresis (PFGE) and "multiple-locus variable-number of tandem repeats analysis" (MLVA) can be replaced by whole genome sequencing or the analytical options can be extended. (bund.de)
  • Across all fields of public healthcare, from animal health and food safety through to the environment ("One Health" concept), microbial whole genome analysis has the potential to become interdisciplinarily harmonised and standardised as a diagnostic investigation technique and therefore to render results from the various areas of speciality comparable. (bund.de)
  • Assigning function to genes in newly sequenced genomes requires highly specific search and comparison methods ( 1 - 4 ). (pnas.org)
  • We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. (nih.gov)
  • The nucleotide sequence APIs visualize and analyze genomes, as well as find specific genes and splice sites within a genome. (programmableweb.com)
  • An alignment of the relevant part of the polypeptide sequence, comprising the presumed signature residues at positions 108, 120, 138, 163 and 199, is shown in the Figure, panel B, for all FIPV and FECV genomes sequenced in this study. (cdc.gov)
  • GENOME analysis has been used to establish the evolutionary and homoeologous relationships of the three genomes (AA, BB, and DD) that make up hexaploid wheat ( Triticum aestivum L.). Each of the 21 chromosomes has been identified and characterized by S ears (1954) ( 1966 ) with respect to genomic and homoeologous relationships. (genetics.org)
  • Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. (sciencemag.org)
  • As more species' genomes are sequenced, computational analysis of these data has become increasingly important. (cshlpress.com)
  • Prepare sequencing-ready libraries for small genomes like mitochondrial DNA in less than 90 minutes. (illumina.com)
  • Due to modern techniques of DNA analysis, many genomes have been sequenced and analyzed. (wikibooks.org)
  • Sequencing genomes allow scientists to identify homologous proteins and establish evolutionary relationships. (wikibooks.org)
  • The tables from below are taken from Wikipedia's list of sequenced eukaryotic genomes . (wikibooks.org)
  • Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. (mdpi.com)
  • Methodologies used include sequence alignment, searches against biological databases, and others. (wikipedia.org)
  • Nowadays, there are many tools and techniques that provide the sequence comparisons (sequence alignment) and analyze the alignment product to understand its biology. (wikipedia.org)
  • Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score. (wikipedia.org)
  • There are two main types of sequence alignment. (wikipedia.org)
  • Pair-wise sequence alignment only compares two sequences at a time and multiple sequence alignment compares many sequences. (wikipedia.org)
  • Popular tools for sequence alignment include: Pair-wise alignment - BLAST Multiple alignment - ClustalW, PROBCONS, MUSCLE, MAFFT, and T-Coffee. (wikipedia.org)
  • A common use for pairwise sequence alignment is to take a sequence of interest and compare it to all known sequences in a database to identify homologous sequences. (wikipedia.org)
  • Rather than using a single sequence, profile methods use a multiple sequence alignment to encode a profile which contains information about the conservation level of each residue. (wikipedia.org)
  • Finally, the remaining unassigned proteins may be compared with known protein folds or structures by using sequence-structure alignment or threading methods ( 10 - 16 ). (pnas.org)
  • Sequence Similarity Search (SSS) is a method of searching sequence databases by using alignment to a query sequence. (ebi.ac.uk)
  • It takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs of different individuals into high-confidence sequences, anchors the merged sequences into the reference genome, and finally genotypes all individuals for the discovered insertions. (psu.edu)
  • In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. (nih.gov)
  • Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. (wikipedia.org)
  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome" (PDF). (wikipedia.org)
  • HMMER is a suite of several programs for biological sequence alignment and database homology search. (ubuntu.com)
  • It uses probabilistic models called "profile hidden Markov models" (profile HMMs) to represent the likely evolutionary homologs of a single sequence or a multiple alignment of a sequence family. (ubuntu.com)
  • Suppose you have a multiple sequence alignment of a sequence family of interest, and you want to search a sequence database for additional homologs. (ubuntu.com)
  • You can construct a manageably small alignment of a representative set of sequences, build a profile with hmmbuild , and use the hmmalign program to align any number of sequences to that profile. (ubuntu.com)
  • Then, I will discuss sequence comparison, that does not need an alignment (alignment free methods). (edu.au)
  • A finish with local alignment, probability theory of sequence comparison and database search. (edu.au)
  • This approach is more consistent approach to analysis of homologous sequences over the use optimization alignment, that uses optimization to deal with insertion-deletions, but statistics to deal with substitution events. (edu.au)
  • 1. Pairwise Global Alignment of Sequences. (wiley.com)
  • 1.9 Alignment Score and Sequence Distance. (wiley.com)
  • Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by comparison of sub-type specific sequence profiles, and analysis of positional entropy in the alignment. (umd.edu)
  • Is the Subject Area "Sequence alignment" applicable to this article? (plos.org)
  • M.S. Waterman and R. Jones , Consensus Methods for DNA and Protein Sequence Alignment. (elsevier.com)
  • D.-F. Feng and R.F. Doolittle , Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences. (elsevier.com)
  • G.J. Barton , Protein Multiple Sequence Alignment and Flexible Pattern Matching. (elsevier.com)
  • G.M. Landau, U. Vishkin, and R. Nussinov , Fast Alignment of DNA and Protein Sequences. (elsevier.com)
  • I will then continue to describe my recent and ongoing algorithmic work on clustering, error correction, and alignment of long-read transcriptome sequencing data. (kth.se)
  • The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. (cambridge.org)
  • In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. (wikipedia.org)
  • SEALS - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics. (bioinformatics.org)
  • Social sequence analysis is a special application of sequence analysis , a set of methods that were originally designed in bioinformatics to analyze DNA , RNA , and peptide sequences. (wikipedia.org)
  • Suitable for bioinformatics, text analysis and other applications, the sequence analysis tools operate on both strings and general lists, and are fully integrated into the general Mathematica programming and visualization system-in all cases yielding results that are organized for further computation. (wolfram.com)
  • His main research interests are in the design and analysis of approximation algorithms for NP-hard optimization problems, particularly in the area of bioinformatics. (wiley.com)
  • He served as the co-Chair of International Symposium on Bioinformatics Research and Applications (2005-2016) and the Workshop on Computational Advances in Next-Generation Sequencing (2011-2015). (wiley.com)
  • Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat, Cufflinks and the CummeRbund Bioconductor package. (wikipedia.org)
  • We are filling a need but, most importantly, every project has access to our in-depth expertise in sequencing and bioinformatics," stated Steve McPhail CEO and President of Expression Analysis. (fiercebiotech.com)
  • Technological advancements in bioinformatics are anticipated to provide lucrative opportunities to this vertical and hence propel growth of the global NGS data analysis market in the near future. (openpr.com)
  • Frankfurt Prime Standard: QIA) and to provide QIAGEN's Ingenuity® Variant Analysis™ in integrated bioinformatics for all customers of BGI's sequencing services. (eurekalert.org)
  • Coupling BGI's world-class sequencing with the deep bioinformatics of Ingenuity Variant Analysis will give researchers an enhanced, integrated way to seamlessly move quickly from raw data to valuable insights. (eurekalert.org)
  • Click here to view the growing list of universities adopting Bioinformatics: Sequence and Genome Analysis, Second Edition for course use. (cshlpress.com)
  • New chapters in this second edition cover statistical analysis of sequence alignments, computer programming for bioinformatics, and data management and mining. (cshlpress.com)
  • In conclusion, the second edition of Bioinformatics: Sequence and Genome Analysis is an excellent textbook for bioinformatics introductory courses for both life sciences and computer science students, and a good reference for current problems in the field and the tools and methods employed in their solution. (cshlpress.com)
  • Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing. (cambridge.org)
  • In 1969 the analysis of sequences of transfer RNAs were used to infer residue interactions from correlated changes in the nucleotide sequences, giving rise to a model of the tRNA secondary structure. (wikipedia.org)
  • There are millions of protein and nucleotide sequences known. (wikipedia.org)
  • The Center for Biological Sequence Analysis offers a collection of SOAP-based APIs for working with nucleotide sequences, amino acid sequences, and small molecules. (programmableweb.com)
  • When compared by phylogenetic analysis, the nucleotide sequences of FIPV and FECV M genes distributed into paraphyletic patterns rather than in monophyletic clusters (Figure, panel A). Thus, as we observed earlier for the 3c gene ( 10 ), M gene sequences generally clustered according to the cattery from where they originated, irrespective of their pathotype (e.g. (cdc.gov)
  • In this study, the complete nucleotide sequences of seven bla IMP - or bla VIM -carrying IncHI5 plasmids from Klebsiella pneumoniae , K. quasipneumoniae , and K. variicola were determined and compared in detail with all the other four available sequenced IncHI5 plasmids. (frontiersin.org)
  • This webinar focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use, input formats, how to change parameters and how to interpret the results. (ebi.ac.uk)
  • The hmmemit program generates (simulates) "homologous" sequences by sampling from a profile. (ubuntu.com)
  • In this lecture I will focus on the basic models and how to formulate a dynamical programming algorithm that can calculate the probability of 2 homologous sequences and define a distribution on all possible alignments. (edu.au)
  • Next Generational Sequencing (NGS) technologies, such as Illumina/Solexa, AB SOLiD and 454 Pyrosequencing are revolutionizing the acquisition of genomics data. (utoronto.ca)
  • This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics. (sciencemag.org)
  • First fully validated sequencing system for forensic genomics. (illumina.com)
  • Thus, sequence analysis can be used to assign function to genes and proteins by the study of the similarities between the compared sequences. (wikipedia.org)
  • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids ", by Durbin et al. (rice.edu)
  • These protein sequences then are compared with ( i ) databases of individual protein sequences, ( ii ) databases of protein consensus sequences, or ( iii ) families of aligned proteins ( 4 - 9 ). (pnas.org)
  • ChIP-seq, short for chromatin immunoprecipitation sequencing, combines chromatin immunoprecipitation with real-time next generation sequencing to identify genomic binding sites that proteins such as transcription factors associate with. (news-medical.net)
  • Since proteins are attractive targets for developing drugs, efforts are now underway to map sequences and assign functions to many novel proteins. (wiley.com)
  • This book takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective. (wiley.com)
  • Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
  • This report investigates the possibility of using signal processing techniques in the analysis of biological sequences: DNA, RNA and proteins. (psu.edu)
  • S. Karlin, B.E. Blaisdell, and V. Brendel , Identification of Significant Sequence Patterns in Proteins. (elsevier.com)
  • Two of these, ORFs 2 and 3, appear to code for low-molecular-weight proteins containing amino acid sequences sharing homology with several gram-positive bacterial DNA-binding proteins. (asm.org)
  • Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. (mdpi.com)
  • Previous phylogenetic analyses of 16S rRNA, recA , gyrB , rpoB , and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. (springer.com)
  • The housekeeping gene sequences were provided from the ongoing sequencing project of B. unamae MTl-641 T , B. tuberum STM678 T , B. silvatlantica SRMrh-20 T , and B. silvatlantica PVA5 from a project, funded in part by the U.S. National Science Foundation (Grant IOB-0537497) to George Weinstock (Washington University, St. Louis, MO) and AMH. (springer.com)
  • Ait-Tayeb L, Lefevre M, Passet V, Diancourt L, Brisse S, Grimont PAD (2008) Comparative phylogenies of Burkholderia , Ralstonia , Comamonas , Brevundimonas and related organism derived from rpoB , gyrB and rrs gene sequences. (springer.com)
  • Phylogenetic tree of 16S rRNA gene sequences from Iron Mountain community genome sequencing (red) and selected sequences from cultivated organisms. (nih.gov)
  • 9 ). GenBank accession numbers for the FCoV M gene sequences determined in this study are HQ738691-HQ738733. (cdc.gov)
  • For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. (springer.com)
  • However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. (diva-portal.org)
  • Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased exponentially. (wikipedia.org)
  • In sociology, sequence methods are increasingly used to study life-course and career trajectories, patterns of organizational and national development, conversation and interaction structure, and the problem of work/family synchrony. (wikipedia.org)
  • Development of statistical methods and algorithms for RNA-seq data analysis, including single-cell RNA-seq data. (upenn.edu)
  • Focus is on the development of methods for isoform expression quantification, differential expression, differential alternative splicing, and eQTL analyses. (upenn.edu)
  • Many popular sequence similarity methods calculate expectation values that can be used together with a threshold to guarantee a specific level of false predictions. (pnas.org)
  • Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis , expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. (springer.com)
  • After being introduced to the social sciences in the 1980s and a period of slow growth during the 1990s, social sequence methods have become increasingly prevalent. (wikipedia.org)
  • Sequence analysis methods were first imported into the social sciences from the biological sciences by the University of Chicago sociologist Andrew Abbott in the 1980s, and they have since developed in ways that are unique to the social sciences. (wikipedia.org)
  • The use of sequence methods was initially met with criticism by sociologists who objected to the descriptive and data-reducing orientation of early sequence methods, as well as to a lack of fit between bioinformatic sequence methods and uniquely social phenomena. (wikipedia.org)
  • [35] [36] Since 2000 there has been a surge of interest in refining sequence methods, leading to some major improvements in social sequence methods. (wikipedia.org)
  • That debate has given rise to several methodological innovations that address limitations of sequence comparison methods that were developed in the 20th century. (wikipedia.org)
  • Sociological Methods & Research organized another special issue on social sequence analysis in 2010, leading to what scholars have dubbed the "second wave" of sequence analysis. (wikipedia.org)
  • While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area. (nih.gov)
  • Different marker methods can give different views of diversity, depending upon the evolutionary parameters of the underlying DNA sequence variation. (genetics.org)
  • This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. (wiley.com)
  • Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. (wiley.com)
  • The development of NGS is forcing a reconsideration of the computational methods used for genome analysis, with the problems of read mapping and genome assembly becoming much more complex. (utoronto.ca)
  • Simultaneously, NGS is enabling the development of methods to address problems which were previously not addressed with genome sequencing, such as the prediction of structural or copy number polymorphisms. (utoronto.ca)
  • In this class we will explore the features of NGS data that make it different from classical sequencing data, and try to determine what are the possible methods to address some of these differences. (utoronto.ca)
  • In present times, a greater level of understanding is demanded due to the complexities involved in genomic research, than those offered by old-style DNA sequencing methods. (openpr.com)
  • The introduction of NGS methods in combination with increasing clinical diagnosis for personalized treatment of many diseases, and genomic research are in need of fast and precise algorithms and sequencing interpretation tools which can analyze data faster. (openpr.com)
  • The introduction of NGS methods combined with their increasing adoption in clinical diagnosis, genomic research, and for personalized treatment of several diseases are bolstering the demand for precise and rapid sequencing interpretation tools and algorithms that can expedite data analysis. (openpr.com)
  • Both are methods for investigating whether or not a sequence diagram specification is a correct refinement of another sequence diagram specification. (uio.no)
  • Further, we extend the operational semantics with support for one class of these basic properties, namely real-time properties, and outline how the operation semantics extended with time can be applied to make methods for timed analysis of sequence diagram specifications. (uio.no)
  • In addition, the Human Genome Project facilitated the development of technologies for high throughput sequencing of DNA and enhanced methods for DNA sequence analysis. (frontiersin.org)
  • Combinatorial pattern matching methods are typically the workhorse of computational molecular biology applications, where the raw data to be analysed are DNA, RNA or protein sequences. (cwi.nl)
  • I will discuss heuristic methods used to align a large number of sequences. (edu.au)
  • The increasing number and diversity of protein sequence families requires new methods to define and predict details regarding function. (umd.edu)
  • During the course of the project, several methods for extracting the features from the spectra of biological sequences and several types of classifiers were tested. (psu.edu)
  • Results indicate that signal processing methods may be very suitable for analyzing biological sequences. (psu.edu)
  • T. Gojobori, E.N. Moriyama, and M. Kimura , Statistical Methods for Estimating Sequence Divergence. (elsevier.com)
  • This sheer volume of available data makes advanced computer methods ess- tial to analysis, and a familiarity with computers and sequence ana- sis software a vital requirement for the researcher involved with DNA sequencing. (springer.com)
  • Items related to Deep Sequencing Data Analysis (Methods in Molecular. (abebooks.com)
  • In this thesis, we present probabilistic models and methods for orthology analysis and species tree inference, while accounting for evolutionary factors such as gene duplication, gene loss, and sequence evolution. (diva-portal.org)
  • It offers a sound, clear, and rich overview of computer science methods for the challenge of today's biological sequence analysis. (cambridge.org)
  • Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation. (springer.com)
  • The factor propelling and challenging the global next generation sequencing data analysis market and recommendations on how to overcome the challenges have also been presented in this study. (openpr.com)
  • When seen from a geographical aspect, due to the presence of some established market players in North America, it is likely to surface as one of the lucrative regions supplementing the growth of the global next generation sequencing data analysis market. (openpr.com)
  • By statistically assessing how well database and query sequences match one can infer homology and transfer information to the query sequence. (ebi.ac.uk)
  • C.B. Lawrence , Use of Homology Domains in Sequence Similarity Detection. (elsevier.com)
  • Novel sequence inser-tions, insertions without similarity to a human reference genome, have received less attention than other types of SVs due to the computational challenges in their detection from short read sequenc-ing data, which inherently involves de novo assembly. (psu.edu)
  • By consequence, many computational biologists have intensified studies in order to understand the content of these sequences and, in some cases, to search for association to disease. (springer.com)
  • This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. (wiley.com)
  • Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. (wiley.com)
  • In this talk, I will present my research on algorithms to reduce the computational bottleneck in some common bioinformatic problems encountered in genome and transcriptome sequence analysis. (kth.se)
  • Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. (diva-portal.org)
  • This book will be a new reference text for string data structures and algorithms, and their applications in computational molecular biology and genome analysis. (cambridge.org)
  • By applying emotif to all of these alignments, we have generated a database called identify , which contains more than 50,000 sequence motifs with specificities varying from one expected false positive prediction in 10 5 tests to as low as one expected false positive prediction in 10 10 tests. (pnas.org)
  • and to automatically construct large multiple alignments (i.e. with an effectively unlimited number of sequences) using a profile representative of a sequence family. (ubuntu.com)
  • Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. (umd.edu)
  • The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows-Wheeler indexes, graph algorithms and a number of advanced omics applications. (cambridge.org)
  • The complete sequence of pMRC01 provides important information about these industrially relevant phenotypes and gives insight into the structure, function and evolution of large Gram-positive conjugative plasmids in general. (ingentaconnect.com)
  • The completely sequenced pMRC01 plasmid should also provide a useful framework for the design of novel plasmids to be incorporated into starter strain improvement programmes for the dairy industry. (ingentaconnect.com)
  • The carbapenemase genes bla IMP-4 , bla IMP-38 and bla VIM-1 were identified within various class 1 integrons from ARI-A or ARI-B of the seven plasmids sequenced in this study. (frontiersin.org)
  • In order to create closed reference genome sequences and plasmids, the Study Centre also makes use of devices that can generate long read lengths. (bund.de)
  • In general, the matches in the database are ordered to show the most closely related sequences first, followed by sequences with diminishing similarity. (wikipedia.org)
  • Find clusters of DNA sequences based on their global similarity to two reference sequences. (wolfram.com)
  • Inferring functional relationships between sequences is performed via comparing a sequence to a sequence database to detect regions of significant similarity or via extracting patterns (motifs), which are significantly overrepresented in a set of sequences. (cwi.nl)
  • Considering the four families above, and a sequence identity threshold of 30 %, our best method gives an accuracy of 96 % compared to 80 % obtained for sequence similarity and 74 % for BLAST. (umd.edu)
  • The best method gives an average accuracy of 94 % compared to 68 % for sequence similarity and 79 % for BLAST. (umd.edu)
  • Sequence variation between strains of A. phagocytophilum (90 to 100% identity at the nucleotide level and 92 to 100% similarity at the protein level) was higher than in A. marginale . (asm.org)
  • Differential expression analysis for sequence count data. (nih.gov)
  • High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. (nih.gov)
  • These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. (springer.com)
  • Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. (springer.com)
  • The Plant Image Analysis API data can be accessed using a GET request that is constructed from a custom URL. (programmableweb.com)
  • Learn about the advantages of targeted single-cell analysis for designing gene panels and maximizing data accuracy with this eBook from The Scientist and BD Biosciences. (the-scientist.com)
  • Next-generation sequencing-based single-cell whole transcriptome amplification analysis techniques can overcome this limitation, but they are not always cost-effective and parsing the large amounts of data obtained to access the relevant portions can take significant amounts of time. (the-scientist.com)
  • Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species. (genetics.org)
  • The data sets that result from marker analysis of germplasm samples are often represented by trees, with the summed branch lengths separating any two samples taken as a measure of their relatedness. (genetics.org)
  • Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. (wiley.com)
  • Part III is devoted to analysis of RNA-seq data. (wiley.com)
  • Hence, our data do not confirm the diagnostic potential of the M protein sequence nor do they support the suggested role of the membrane protein in FIP pathogenesis ( 9 ). (cdc.gov)
  • http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn-1.3-4.fc15.src.rpm Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. (redhat.com)
  • Expression Analysis offers solutions for challenging specimens such as whole blood and FFPE tissues, as well as nucleic acid isolation and data analysis services. (fiercebiotech.com)
  • These platforms offer much reduced costs and an increased speed of data acquisition, but the length of the sequences acquired is much reduced, from 500-1000 base pairs, to as little as 25 base pairs per read. (utoronto.ca)
  • In this investigation of an acute HIV infection in a patient with chronic kidney disease who received care in a hospital and other health care settings, epidemiologic and nucleotide sequence data support likely health care-associated transmission. (cdc.gov)
  • In this module we will be studying sequence data quality control as well as ChIP-Sequence Analysis with MACS. (coursera.org)
  • and data analysis, storage, and management. (openpr.com)
  • However, dearth of skilled professionals and problems associated with storage of sequencing data restrain the market growth. (openpr.com)
  • The Research Report on " Next Generation Sequencing (NGS) Data Analysis Market - Global Industry Analysis, Size, Share, Trends, Analysis, Growth, and Forecast 2017 - 2025", issued by TMR Research, includes a detailed qualitative and quantitative analysis of the market, with the help of information collected from market participants operating across key sectors of the market value chain. (openpr.com)
  • Using industry-centric tools, such as SWOT analysis and Porter's Five Forces analysis, readers are given a 360-degree overview of where the NGS data analysis market will stand in the near future. (openpr.com)
  • Due to constant developments in data integration and cloud computing solutions, data handling bottlenecks are effectively being addressed, involving a sizeable volume analysis of high throughput sequence data. (openpr.com)
  • Concurrent drop in prices and high genetic data output are few of the main causes behind the rise in the scope of sequencing projects. (openpr.com)
  • The continuous advancements in cloud computing and data integration solutions are effectively addressing data handling bottlenecks, which involves analyzing a sizeable volume of high-throughput sequence data. (openpr.com)
  • Moreover, the scope of sequencing projects is expected to rise due to the high genetic data output and concurrent drop in the prices of sequencing. (openpr.com)
  • Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. (frontiersin.org)
  • Get more powerful data from single cells - detect more transcripts with the same sequencing depth, including both mRNA and lncRNA, providing deeper insights into the transcriptome and unveiling the expression of important regulatory RNAs. (qiagen.com)
  • Algorithms and Data Structures for Sequence Analysis In this subgroup of the CWI Life Sciences and Health group, led by Dr. Solon Pissis, we are working on algorithms and data structures for sequence analysis. (cwi.nl)
  • Under the reseller agreement, BGI customers will receive sequencing data generated from their samples through Ingenuity Variant Analysis' secure, cloud-based environment and gain access to its leading comprehensive gene variant data and genomic interpretation applications. (eurekalert.org)
  • BGI's sequencing services are powered by more than 230 DNA sequencers with a data output capability of approximately 16 terabytes per day. (eurekalert.org)
  • Computers have revolutionized the analysis of sequencing data. (springer.com)
  • To reflect this progression, the chapters in our Sequence Data Analysis Guidebook are arranged, not by software package, but by fimction. (springer.com)
  • The sequence data from these four clones were evaluated by six scientists, who analyzed them from the point of view of the community of scientists who use genomic data. (mit.edu)
  • Several of the sequence producers also retrospectively analyzed data from previously completed projects. (mit.edu)
  • It will be important for the data used to generate the draft sequence to be annotated as to quality, especially as quality tends to be worse at contig ends. (mit.edu)
  • mtDNA analysis enables coroner and medical examiner laboratories to extract genetic data from small forensic samples found in less than ideal condition. (illumina.com)
  • Enables streamlined variant analysis of d-loop and whole mitochondrial DNA sequence data. (illumina.com)
  • Enables simplified visualization of d-loop and whole mitochondrial DNA sequence data. (illumina.com)
  • Sequencher is packed with proprietary algorithms and peer-reviewed favorites that generate results for Sanger , Next-Gen Sequencing (NGS) , and RNA-Seq sequence data. (genecodes.com)
  • And, for those experiments where you are looking for concordance between your RNA-Seq and Microarray data, shouldn't you have the concordance in your analysis software as well? (genecodes.com)
  • DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gen- ated. (springer.com)
  • This two-part work on Analysis of Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or p- tein) sequences. (springer.com)
  • September 27, 2018 -- As Next Generation Sequencing (NGS) technology develops, the analysis and interpretation of NGS data will prove to be one of the most complex aspects of transforming NGS data into meaningful results. (scienceboard.net)
  • Tertiary analysis, which follows primary and secondary analysis of the data, is among the most challenging steps. (scienceboard.net)
  • QIAGEN's NGS software platform serves all stages of NGS data analysis, including tertiary analysis. (scienceboard.net)
  • A phylogenetic tree is used to model gene evolution and species evolution using molecular sequence data. (diva-portal.org)
  • This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. (cambridge.org)
  • Probably the most important achievement of ChIP-Seq is the population-level analysis of interactions between protein and DNA. (news-medical.net)
  • The new service will be offered on the Illumina GA II and will include the following applications: Shotgun Sequencing, ChIP Seq, mRNA Seq and small RNA Seq. (fiercebiotech.com)
  • The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia . (springer.com)
  • 9 ). Their conclusion was based on sequence analyses of parts of the viral genome including the matrix (M) gene, phylogenetic analysis of which revealed reciprocal monophyly of the sequences obtained from FIP cases versus those of asymptomatic FECV-infected animals. (cdc.gov)
  • Because the analysis of the W. succinogenes genome also revealed genes related to soil- and plant-associated bacteria such as the nif genes, W. succinogenes may represent a member of the epsilon proteobacteria with a life cycle outside its host. (pnas.org)
  • For example, analysis of DNA binding sites in the mouse brain has led to the identification of new tissue-specific regulatpry areas (enhancers) of genes. (news-medical.net)
  • Toucan - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes. (bioinformatics.org)
  • tRNAscan-SE - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. (bioinformatics.org)
  • In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD , gltB , lepA , and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. (springer.com)
  • In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. (uniprot.org)
  • Several of the discussants emphasized that coding sequences or genes are by no means the only sequence features that will be studied. (mit.edu)
  • To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. (jcvi.org)
  • A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat ( Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. (genetics.org)
  • Revealing the evolution and genetic diversity of sequences and organisms Identification of molecular structure from sequence alone In chemistry, sequence analysis comprises techniques used to determine the sequence of a polymer formed of several monomers. (wikipedia.org)
  • The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. (springer.com)
  • THE genetic diversity of a species is the sum of its total DNA sequence variation, resulting from millions of years of cumulative mutation, recombination, and selection. (genetics.org)
  • In this paper, the evolvable reasoning hardware and its genetic-algorithm-based design methodology is applied to the analysis of genomic sequences. (actapress.com)
  • For the characterization of genetic heterogeneity in this species, the homologue of Anaplasma marginale major surface protein 4 gene ( msp4 ) was identified, and the coding region was PCR amplified and sequenced from a variety of sources, including 50 samples from the United States, Germany, Poland, Norway, Italy, and Switzerland and 4 samples of A. phagocytophilum -like organisms obtained from white-tailed deer in the United States. (asm.org)
  • Applications covered in the study include de novo transcriptome assembly, expression profiling analysis, variant calling & transcriptome epigenetics, and small RNA sequencing. (openpr.com)
  • Platforms utilized include Affymetrix GeneChip® and GeneTitan®, Applied Biosystems' Taqman, Fluidigm's Biomark and Access Array Systems, Illumina BeadChip® and Genome Analyzer, NanoString Technologies nCounter® Analysis System, RainDance Technologies RDT 1000 and, in the near future, the Pacific Biosciences™ PacBio RS. (fiercebiotech.com)
  • January 16th -- Next Generation Sequencing Platforms. (utoronto.ca)
  • Availability of the reference human genome sequence enabled the generation of oligonucleotide probes and short sequence markers (SNPs) mapped to specific chromosome positions that could then be used to generate microarray platforms to analyze DNA from specific patients to search for genomic copy number variants and genomic structural variants. (frontiersin.org)
  • Based on technology, the market is classified into sequencing by synthesis (SBS), ion semiconductor sequencing, single-molecule real-time (SMRT) sequencing, and nanopore sequencing. (openpr.com)
  • Illumina NGS technology, sequencing by synthesis (SBS), offers fast results and deep coverage of areas of interest. (illumina.com)
  • Illumina next-generation sequencing (NGS) has the potential to transform mitochondrial DNA (mtDNA) analysis. (illumina.com)
  • Indexed libraries that are ready for Illumina sequencing can be prepared in less than 4 hours using the SMARTer Stranded RNA-Seq Kit protocol. (clontech.com)
  • Integrated with Illumina sequencing -Incorporates indexes and Illumina adapters in the workflow. (clontech.com)
  • Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. (genetics.org)
  • Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. (genetics.org)
  • Sequence analysis of the protective and hypertensive BP loci revealed 1433 and 2063 variants between Dahl salt-sensitive/Mcwi and Brown Norway rats, respectively. (ahajournals.org)
  • Sequence comparison among Dahl salt-sensitive, Dahl R, and Brown Norway reduced the number of candidate variants in the 2 BP loci by 42% for further study. (ahajournals.org)
  • This book presents molecular biology knowledge and mathematical theories of frequently-used algorithms in sequence comparison, gene finding, sequence evolution and structuring phylogenetic tree. (degruyter.com)
  • Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. (nih.gov)
  • Detailed analyses at the molecular level will reveal the evolution of chromosome structure and the distribution and physical location of additional breakpoints and rearrangements within homoeologous group 4 chromosomes of hexaploid wheat. (genetics.org)
  • Complex biological sequence analysis and comparison have been playing important roles in molecular studies. (hindawi.com)
  • The deduced amino acid sequence indicates that the unprocessed fructosyltransferase gene product has a molecular weight of 87,600. (asm.org)
  • This course teaches the individual how to analyze DNA and protein sequences using computer software. (bioinformatics.org)
  • Suppose you have sequence(s) that you want to analyze using a HMMER-based profile HMM database like Pfam ( http://pfam.sanger.ac.uk ). (ubuntu.com)
  • The report offers a quantitative analysis from 2017 to 2023, which is expected to enable the stakeholders to capitalize on prevailing market opportunities. (openpr.com)
  • Other fully sequenced organisms include: roundworm, fruitfly, pufferfish (first vertebrate to be sequenced after humans), and Arabidopsis thaliana . (wikibooks.org)
  • Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. (wikipedia.org)
  • These organisms belong together with Wolinella succinogenes to the epsilon subclass of the proteobacteria, as has been demonstrated by 16S rRNA analysis ( 5 , 6 ). (pnas.org)
  • The gene is ideal for sequence-based identification of these organisms, particularly in mixed samples, due to the presence of conserved and highly variable regions. (nanoporetech.com)
  • By narrowing down to a specific region of interest, all the organisms present in the sample can be seen without sequencing unnecessary regions of the genome, making the analysis quicker and more economical. (nanoporetech.com)
  • The workflow is designed to BLAST basecalled sequence against the NCBI 16S bacterial database , which contains over 20,000 16S sequences from different organisms. (nanoporetech.com)
  • We also completely sequenced versions of the large chromosome-5-specific internal duplications. (uniprot.org)
  • Anyone interested in learning about algorithms and their use in biological sequence analysis. (rice.edu)
  • Successful experiments illustrated that CHC is an effective tool of biological sequence analysis and comparison. (hindawi.com)
  • High-throughput sequencing has revolutionised the field of biological sequence analysis. (cambridge.org)
  • The rapid advances in sequencing technologies require parallel advances in bioinformatic algorithms. (kth.se)
  • This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. (nih.gov)
  • By operational analysis we mean analysis based on a characterization of the executions of sequence diagrams, or in other words an operational semantics for sequence diagrams. (uio.no)
  • Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. (sciencemag.org)
  • These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. (nih.gov)
  • UGENE - a free and open source DNA and protein sequence analysis tool. (bioinformatics.org)
  • Oxford Nanopore also provides a complete 16S analysis workflow, enabling users to classify mixed samples and obtain accurate results for single reads at the genus level. (nanoporetech.com)
  • Its simple workflow can quickly deliver forensic mtDNA analysis results, potentially speeding up investigations. (illumina.com)
  • Today, complexities involved in genomic research demands a higher level of understanding than what is offered by traditional DNA sequencing methodologies. (openpr.com)
  • Amino terminal amino acid sequence analysis of the 30-kDa inhibitor demonstrated 86% identity to human TIMP-1 for the first 22 amino acids while the sequence of the 20-kDa inhibitor was identical to that of human TIMP-2 for the first 22 residues. (uniprot.org)
  • P. Argos and M. Vingron , Sensitivity Comparison of Protein Amino Acid Sequences. (elsevier.com)
  • Shuffling of nucleotides at the third synonymous codon sites which retained nucleotide composi- tion and amino acid sequence of the native mRNAs affected nucleotide base pairing to some extend due to changes in codon context (Table 1). (psu.edu)
  • A typical streptococcal signal sequence is present at the amino terminus of the protein. (asm.org)
  • J.C.W. Shepherd , Ancient Patterns in Nucleic Acid Sequences. (elsevier.com)
  • R. Staden , Searching for Patterns in Protein and Nucleic Acid Sequences. (elsevier.com)
  • In recent decades, exome sequencing has primarily been used in patient studies. (frontiersin.org)
  • Examples of cases where exome sequencing has facilitated diagnosis and led to improved medical management are presented. (frontiersin.org)
  • Exhaustive analysis of the RNA sequencing market by type helps to understand the types of sequencing technologies that are currently being used along with the variants that are expected to gain prominence in the future. (openpr.com)
  • Pharmogenetic variants detected by DNA sequence analysis are gaining in importance and are particularly relevant to personalized and precision medicine. (frontiersin.org)
  • One strategy for mapping blood pressure (BP) variants is by linkage analysis using inbred rat strains. (ahajournals.org)
  • On the other extreme, there are low effect sized common variants that can be detected by association studies and then in the middle are the low effect and relatively uncommon which can be detected by sequencing of enriched families that include multiple relatives. (hstalks.com)
  • Cellular heterogeneity plays a critical role in systems and pathologies, but many genomic analysis techniques derive their findings from multicellular samples, potentially burying key information from individual cells or rare subsets. (the-scientist.com)
  • Detection of sequence patterns with interfaces at ExPASy (Switzerland). (rcsb.org)
  • Motivation: The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. (psu.edu)
  • IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. (nih.gov)
  • Estimates of evolutionary divergence between 16S sequences in Borrelia spp. (cdc.gov)
  • The first step of inferring evolutionary relationships between sequences is the pairwise or multiple comparison of these sequences. (cwi.nl)
  • Methylation analysis of gene promoters using bilsulfite treatment of DNA and comparative DNA sequence analysis. (bio-medicine.org)
  • The programs can be 'piped' into one another, allowing the simultaneous identification of promoters, coding exons and repetitive sequence using one command line. (bio.net)
  • Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms. (harvard.edu)
  • Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. (sciencemag.org)
  • Suppose you want to align lots of sequences. (ubuntu.com)
  • During the past summer, the NHGRI-supported sequencing centers assessed strategies to generate a shotgun product that would constitute a working draft' of the human genome. (mit.edu)
  • Sequencing centers produced several versions of possible working drafts, using a sample of four BAC clones containing inserts whose finished sequence is already known and annotated. (mit.edu)
  • All three programs accept sequence in plain, Fasta, EMBL or GenBank format, and output the sequence, with an added feature table, in EMBL or GenBank format. (bio.net)
  • W.R. Pearson , Rapid and Sensitive Sequence Comparison with FASTP and FASTA. (elsevier.com)
  • Community-wide analysis of microbial genome sequence signatures. (nih.gov)
  • Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities. (nih.gov)
  • Furthermore, analysis of the full-length 16S rDNA gene using long-read nanopore sequencing has been shown to enhance the resolution of microbial characterisation . (nanoporetech.com)
  • in the field of microbial next generation sequencing (NGS) techniques of the 2nd and 3rd generation. (bund.de)
  • The process involves first identifying all ORFs or coding regions in the genome and translating them into putative protein sequences. (pnas.org)
  • identify can be used to scan newly sequenced ORFs from genomic sequences for function. (pnas.org)
  • Sequencing of the regions flanking the gene revealed the presence of four other putative open reading frames (ORFs). (asm.org)
  • Sequences for which only partial coverage of the 16S rRNA gene was obtained are not shown, including ARMAN-5, a gammaproteobacterium, additional Actinobacteria, and Sulfobacillus -like sequences. (nih.gov)
  • Two important algorithms for aligning pairs of sequences are the Needleman-Wunsch algorithm and the Smith-Waterman algorithm. (wikipedia.org)
  • The first eukaryotic genome to be sequenced is that of Saccharomyces cerevisiae ( S. cerevisiae ) in 1996, and it is commonly known as brewer's yeast. (wikibooks.org)
  • The following chap- ters describe the process of aligning multiple sequences in order to assemble overlapping fragments into sequence contigs to compare similar sequences from different sources. (springer.com)
  • In marketing, sequence analysis is often used in analytical customer relationship management applications, such as NPTB models (Next Product to Buy). (wikipedia.org)
  • With SGS you can be sure that your analysis will meet ICH Q6B guidelines to support new marketing applications. (sgs.com)
  • Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. (frontiersin.org)
  • Applications of DNA sequencing to diagnosis and therapeutics of cancer are presented. (frontiersin.org)
  • Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived cell free DNA and exosomes that are present in body fluids. (frontiersin.org)
  • Headquartered in Shenzhen, China, BGI encompasses both private nonprofit research institutes and commercial units for sequencing applications, as well as its affiliated offshoots BGI Americas and BGI Europe. (eurekalert.org)
  • As new NGS applications expand, such as sequencing of newborn children or retesting individuals over their lifetime, the need for such capabilities will become even more evident. (scienceboard.net)