Base sequence. Medical search

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

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).

The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.

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 reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.

Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

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 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.

A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

A highly fluorescent anti-infective dye used clinically as a topical antiseptic and experimentally as a mutagen, due to its interaction with DNA. It is also used as an intracellular pH indicator.

Deoxyribonucleic acid that makes up the genetic material of viruses.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

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.

Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.

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.

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)

The inferior region of the skull consisting of an internal (cerebral), and an external (basilar) surface.

The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.

Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)

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 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.

A genus of ascomycetous fungi of the family Saccharomycetaceae, order SACCHAROMYCETALES.

Condensation products of aromatic amines and aldehydes forming azomethines substituted on the N atom, containing the general formula R-N:CHR. (From Grant & Hackh's Chemical Dictionary, 5th ed)

Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.

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.

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

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 purine base and a fundamental unit of ADENINE NUCLEOTIDES.

An order of fungi in the phylum Ascomycota that multiply by budding. They include the telomorphic ascomycetous yeasts which are found in a very wide range of habitats.

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.

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.

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).

Ribonucleic acid that makes up the genetic material of viruses.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.

A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.

The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.

A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)

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.

Viruses whose host is Escherichia coli.

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.

The rate dynamics in chemical or physical systems.

A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.

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.

A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.

The functional hereditary units of BACTERIA.

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.

The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

The functional hereditary units of VIRUSES.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

Presence of warmth or heat or a temperature notably higher than an accustomed norm.

Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.

Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).

Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.

The sum of the weight of all the atoms in a molecule.

Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

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.

Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.

Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.

The relationships of groups of organisms as reflected by their genetic makeup.

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

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.

Established cell cultures that have the potential to propagate indefinitely.

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.

The process by which a DNA molecule is duplicated.

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.

Neoplasms of the base of the skull specifically, differentiated from neoplasms of unspecified sites or bones of the skull (SKULL NEOPLASMS).

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.

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.

Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.

The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.

The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).

A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).

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.

Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.

The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.

Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

The part of a denture that overlies the soft tissue and supports the supplied teeth and is supported in turn by abutment teeth or the residual alveolar ridge. It is usually made of resins or metal or their combination.

Proteins found in any species of bacterium.

Computer-based representation of physical systems and phenomena such as chemical processes.

Proteins found in any species of virus.

DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.

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.

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.

Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.

Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).

Ketonic amines prepared from the condensation of a ketone with formaldehyde and ammonia or a primary or secondary amine. A Mannich base can act as the equivalent of an alpha,beta unsaturated ketone in synthesis or can be reduced to form physiologically active amino alcohols.

A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.

The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.

A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.

Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/178859)

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing 'fingerprints' of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591--8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3'-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be 'looped out' by small helix imperfections also show some reactivity. (+info)

Marker effects on reversion of T4rII mutants. (2/178859)

The frequencies of 2-aminopurine- and 5-bromouracil-induced A:T leads to G:C transitions were compared at nonsense sites throughout the rII region of bacteriophage T4. These frequencies are influenced both by adjacent base pairs within the nonsense codons and by extracodonic factors. Following 2AP treatment, they are high in amber (UAG) and lower in opal (UGA) codons than in allelic ochre (UAA) codons. In general, 5BU-induced transitions are more frequent in both amber and opal codons than in the allelic ochre codons. 2AP- and 5BU-induced transition frequencies in the first and third positions of opal codons are correlated with those in the corresponding positions of the allelic ochre codons. Similarly, the frequencies of 2AP-induced transition in the first and second positions of amber codons and their ochre alleles are correlated. However, there is little correlation between the frequencies of 5BU-induced transitions in the first and second positions of allelic amber and ochre codons. (+info)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (3/178859)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation. (+info)

Regulation of body length and male tail ray pattern formation of Caenorhabditis elegans by a member of TGF-beta family. (4/178859)

We have identified a new member of the TGF-beta superfamily, CET-1, from Caenorhabditis elegans, which is expressed in the ventral nerve cord and other neurons. cet-1 null mutants have shortened bodies and male tail abnormal phenotype resembling sma mutants, suggesting cet-1, sma-2, sma-3 and sma-4 share a common pathway. Overexpression experiments demonstrated that cet-1 function requires wild-type sma genes. Interestingly, CET-1 appears to affect body length in a dose-dependent manner. Heterozygotes for cet-1 displayed body lengths ranging between null mutant and wild type, and overexpression of CET-1 in wild-type worms elongated body length close to lon mutants. In male sensory ray patterning, lack of cet-1 function results in ray fusions. Epistasis analysis revealed that mab-21 lies downstream and is negatively regulated by the cet-1/sma pathway in the male tail. Our results show that cet-1 controls diverse biological processes during C. elegans development probably through different target genes. (+info)

Activation of systemic acquired silencing by localised introduction of DNA. (5/178859)

BACKGROUND: In plants, post-transcriptional gene silencing results in RNA degradation after transcription. Among tobacco transformants carrying a nitrate reductase (Nia) construct under the control of the cauliflower mosaic virus 35S promoter (35S-Nia2), one class of transformants spontaneously triggers Nia post-transcriptional gene silencing (class II) whereas another class does not (class I). Non-silenced plants of both classes become silenced when grafted onto silenced stocks, indicating the existence of a systemic silencing signal. Graft-transmitted silencing is maintained in class II but not in class I plants when removed from silenced stocks, indicating similar requirements for spontaneous triggering and maintenance. RESULTS: Introduction of 35S-Nia2 DNA by the gene transfer method called biolistics led to localised acquired silencing (LAS) in bombarded leaves of wild-type, class I and class II plants, and to systemic acquired silencing (SAS) in class II plants. SAS occurred even if the targeted leaf was removed 2 days after bombardment, indicating that the systemic signal is produced, transmitted and amplified rapidly. SAS was activated by sense, antisense and promoterless Nia2 DNA constructs, indicating that transcription is not required although it does stimulate SAS. CONCLUSIONS: SAS was activated by biolistic introduction of promoterless constructs, indicating that the DNA itself is a potent activator of post-transcriptional gene silencing. The systemic silencing signal invaded the whole plant by cell-to-cell and long-distance propagation, and reamplification of the signal. (+info)

Molecular cloning and epitope analysis of the peanut allergen Ara h 3. (6/178859)

Peanut allergy is a significant IgE-mediated health problem because of the increased prevalence, potential severity, and chronicity of the reaction. Following our characterization of the two peanut allergens Ara h 1 and Ara h 2, we have isolated a cDNA clone encoding a third peanut allergen, Ara h 3. The deduced amino acid sequence of Ara h 3 shows homology to 11S seed-storage proteins. The recombinant form of this protein was expressed in a bacterial system and was recognized by serum IgE from approximately 45% of our peanut-allergic patient population. Serum IgE from these patients and overlapping, synthetic peptides were used to map the linear, IgE-binding epitopes of Ara h 3. Four epitopes, between 10 and 15 amino acids in length, were found within the primary sequence, with no obvious sequence motif shared by the peptides. One epitope is recognized by all Ara h 3-allergic patients. Mutational analysis of the epitopes revealed that single amino acid changes within these peptides could lead to a reduction or loss of IgE binding. By determining which amino acids are critical for IgE binding, it might be possible to alter the Ara h 3 cDNA to encode a protein with a reduced IgE-binding capacity. These results will enable the design of improved diagnostic and therapeutic approaches for food-hypersensitivity reactions. (+info)

TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. (7/178859)

We report the cloning and characterization of a novel member of the Transcriptional Intermediary Factor 1 (TIF1) gene family, human TIF1gamma. Similar to TIF1alpha and TIF1beta, the structure of TIF1beta is characterized by multiple domains: RING finger, B boxes, Coiled coil, PHD/TTC, and bromodomain. Although structurally related to TIF1alpha and TIF1beta, TIF1gamma presents several functional differences. In contrast to TIF1alpha, but like TIF1beta, TIF1 does not interact with nuclear receptors in yeast two-hybrid or GST pull-down assays and does not interfere with retinoic acid response in transfected mammalian cells. Whereas TIF1alpha and TIF1beta were previously found to interact with the KRAB silencing domain of KOX1 and with the HP1alpha, MODI (HP1beta) and MOD2 (HP1gamma) heterochromatinic proteins, suggesting that they may participate in a complex involved in heterochromatin-induced gene repression, TIF1gamma does not interact with either the KRAB domain of KOX1 or the HP1 proteins. Nevertheless, TIF1gamma, like TIF1alpha and TIF1beta, exhibits a strong silencing activity when tethered to a promoter. Since deletion of a novel motif unique to the three TIF1 proteins, called TIF1 signature sequence (TSS), abrogates transcriptional repression by TIF1gamma, this motif likely participates in TIF1 dependent repression. (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (8/178859)

The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity. (+info)

Numeration systems based on the hyperoperation sequence[edit]. R. L. Goodstein,[2] with a system of notation different from ... This compares to ordinary base-2 representation when the latter is written out in terms of the base b; e.g., in ordinary base-2 ... Note that in this type of base-b hereditary representation, the base itself appears in the expressions, as well as "digits" ... It is closely related to the Ackermann function and especially to the hyperoperation sequence. The idea is based on the fact ...

https://en.wikipedia.org/wiki/Knuth_up-arrow_notation

Sequence-based classification[edit]. Sequence-based classifications are among the most powerful predictive method for ... the sequence-based families have been classified into 'clans' of related structure. Recent progress in glycosidase sequence ... A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of more than 100 ... Glycoside hydrolases may also be classified by sequence or structure based methods.[4] ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase

Complementary base sequence 5 Hormone Receptor 6 Avidin Biotin 7 Calmodulin Calmodulin binding molecule ... WAC is an affinity-based liquid chromatographic technique that separates chemical compounds based on their different weak ... The way that the desired enzyme would be eluted would be from the mixture based on the strong interaction of enzyme and the ... Affinity chromatography is a method of separating biochemical mixture based on a highly specific interaction between antigen ...

https://en.wikipedia.org/wiki/Immunoaffinity_chromatography

Base.Sequence.unfold ~init ~f. [5] Oz {FoldL List Func InitVal}. {FoldR List Func InitVal}. ... foldl(func, initval, sequence). foldr(func, initval, sequence). Mathematica Fold[func, initval, list]. Fold[func, initval, ... sequence. The difference in the signatures is due to the fact that the value of an array. item can be a sequence. , while XPath ... "Base". Jane Street Capital. Retrieved February 26, 2019.. *^ For reference functools.reduce. : import functools. For reference ...

https://en.wikipedia.org/wiki/Fold_(higher-order_function)

Nucleic acid sequence-based amplification, commonly referred to as NASBA, is a method in molecular biology which is used to ... Mugasa, CM; Laurent, T; Schoone, GJ; Kager, PA; Lubega, GW; Schallig, HD (2009). "Nucleic acid sequence-based amplification ... Malek, L.; Sooknanan, R.; Compton, J. (1994). Nucleic acid sequence-based amplification (NASBA). Methods in Molecular Biology. ... Malek, L.; Sooknanan, R.; Compton, J. (1994). Nucleic acid sequence-based amplification (NASBA). Methods in Molecular Biology. ...

https://en.wikipedia.org/wiki/NASBA_(molecular_biology)

2019) based on molecular sequence data. Sites and ages of specimen (complete list): Casimba, Cuba ~1.8 Mya-11,000 years ago. ... It was assigned to Megalonychidae by Matthew (1931) based on morphological considerations, and subsequently moved to ...

https://en.wikipedia.org/wiki/Miocnus

Base sequence of the recognition site". Journal of Molecular Biology. 51 (2): 393-409. doi:10.1016/0022-2836(70)90150-6. PMID ... Kelly determined the DNA sequences recognized by type II restriction enzymes, which subsequently became major tools in ...

https://en.wikipedia.org/wiki/Thomas_J._Kelly_(scientist)

Base-dependent integer sequences. Hidden categories: *Articles lacking in-text citations from September 2010 ... This sequence starts (sequence A020342 in the OEIS): 126, 153, 688, 1206, 1255, 1260, 1395, .... A prime vampire number, as ... There are many known sequences of infinitely many vampire numbers following a pattern, such as: 1530 = 30×51, 150300 = 300×501 ...

https://en.wikipedia.org/wiki/Vampire_number

Sequence OEIS: A092697 in the On-Line Encyclopedia of Integer Sequences.. *. Bernstein, Leon (1968), "Multiplicative twins and ... it will find them in base 8 and base 16 as well. Look at line 15 in Table Two. The fix, when this condition is identified and ... Other bases[edit]. In duodecimal system, the smallest n-parasitic numbers are: (using inverted two and three for ten and eleven ... An n-parasitic number (in base 10) is a positive natural number which can be multiplied by n by moving the rightmost digit of ...

https://en.wikipedia.org/wiki/Parasitic_numbers

Aves: Corvidae) based on nucleotide sequence data. Journal of Avian Biology. 36(3): 222-234. https://www.researchgate.net/ ...

https://en.wikipedia.org/wiki/Sri_Lanka_blue_magpie

Meyer F, Kurtz S, Backofen R, Will S, Beckstette M (2011). "Structator: fast index-based search for RNA sequence-structure ... Meyer F, Kurtz S, Beckstette M (July 2013). "Fast online and index-based algorithms for approximate search of RNA sequence- ... Andrew Xiang Li; Jing Qin; Manja Marz; Christian M. Reidys (2011). "RNA-RNA interaction prediction based on multiple sequence ... Weinberg Z, Ruzzo WL (2006). "Sequence-based heuristics for faster annotation of non-coding RNA families". Bioinformatics. 22 ( ...

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

Xavier Didelot (2010). "Sequence-Based Analysis of Bacterial Population Structures". In D. Ashley Robinson; Daniel Falush; ... Usually used for trees based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each ... Based on a distance matrix relating the n {\displaystyle n} taxa, calculate Q {\displaystyle Q} as follows: where d ( i , j ... Based on the current distance matrix calculate the matrix Q {\displaystyle Q} (defined below). Find the pair of distinct taxa i ...

https://en.wikipedia.org/wiki/Neighbor_joining

Based on the peptide sequence tag approach. MS/MS Ion Search Identify fragment ions from uninterpreted MS/MS data of one or ... Mascot generates a randomized sequence of the same length for every sequence in the target database. The decoy sequence is ... Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (December 1999). "Probability-based protein identification by searching sequence ... Sequence query Combines peptide mass data with amino acid sequence and composition information usually obtained from MS/MS ...

https://en.wikipedia.org/wiki/Mascot_(software)

2000). "Phylogeography of Peromyscus furvus (Rodentia; Muridae) based on cytochrome b sequence data". Molecular Ecology. 9 (12 ...

https://en.wikipedia.org/wiki/Blackish_deer_mouse

The protein sequence is 295 base pairs. Its locus is 7p12.3. It is often found in nuclear and mitochondrial sub cellular ... Within the gene sequence 9 exons are present. C7orf57 has been linked to lupus, pancreatic cancer sporadic amyotrophic lateral ... The promoter is 1125 base pairs long, located between 48024511-48025635. It codes for six transcripts of C7orf57. There are ...

https://en.wikipedia.org/wiki/C7orf57

March 2013). "A sequence-based variation map of zebrafish". Zebrafish. 10 (1): 15-20. doi:10.1089/zeb.2012.0848. PMC 3629779. ... He is best known for sequencing the first Indian genome. He was also instrumental in the sequencing of The first Sri Lankan ... 2014). "Exome sequencing reveals a novel mutation, p.L325H, in the KRT5 gene associated with autosomal dominant Epidermolysis ... His research took a shift to Clinical Genomics in 2009 starting with the sequencing of the first Indian Genome in 2009. Over ...

https://en.wikipedia.org/wiki/Vinod_Scaria

It is based on a recursive sequence. It increases 10% each nice level. It follows a parabolic pattern if graphed, and the niced ... The virtual deadline formula is a future deadline time that is the scaled round robin timeslice based on the nice level offset ... Tasks are ordered (or distributed) and chosen based on the virtual deadline formula in all policies except for the realtime and ... The virtual deadline is based on this exact formula: T = 6 N = 1<. ...

https://en.wikipedia.org/wiki/Brain_Fuck_Scheduler

Compositae, Anthemideae) based on cpDNA sequence variation". Plant Systematics and Evolution. 298 (7): 1407-1414. doi:10.1007/ ... The base of the head is layered with up to 60 or more rough-edged phyllaries. The Leucanthemum head has about 13 to 34 ray ... Some leaves are borne on petioles, and others are sessile, attached to the stem at their bases. They vary in shape, and some ...

https://en.wikipedia.org/wiki/Leucanthemum

Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: 1758-1776. Rohwer JG & Rudolph B. 2005 ... Based on Different Analyses of trnK Intron Sequences. Annals of the Missouri Botanical Garden, 92(2), 153-178. JSTOR Kuijt, J. ... based on different analyses of trnK intron sequences. Annals of the Missouri Botanical Garden 92: 153-178. Kimoto Y, Utami N, ... Based on the trnK intron, a common phylogenetic marker for classifying angiosperms, Rohwer and Rudolph (2005) created a ...

https://en.wikipedia.org/wiki/Cassytha

Naylor G J P, Caira J N, Jensen K, Rosana K A M, White W T, Last P R (2012): A DNA sequence-based approach to the ... based on DNA sequences. Chinese Journal of Oceanology and Limnology, doi:10.1007/s00343-018-7056-2. Pavan-Kumar, A.; Kumar, R ... based on cytochrome-oxidase I gene sequences and spotting patterns. Comptes Rendus Biologies, 336 (4): 221-232.[3] Garman, S ( ... Within the genus Neotrygon, species can be diagnosed by their nucleotide sequence at the CO1, NADH2, and cytochrome b gene loci ...

https://en.wikipedia.org/wiki/Maskray

based on molecular sequences". Mycotaxon. 82: 315-322. Krüger, D.; Petersen, R.H.; Hughes, K.W. (2006). "Molecular phylogenies ... In a 1995 monograph, Maria Núñez and Leif Ryvarden grouped 32 Polyporus species into 6 morphologically-based infrageneric ... Krüger, D.; Gargas A. (2004). "The basidiomycete genus Polyporus-an emendation based on phylogeny and putative secondary ... Polyporales, Basidiomycota) from China based on morphological and molecular data" (PDF). Mycological Progress. 13 (3): 811-817 ...

https://en.wikipedia.org/wiki/Polyporus

Thus, the number Rn = Rn(10) consists of n copies of the digit 1 in base 10 representation. The sequence of repunits base 10 ... Base 9 repunit primes[edit]. There are no base 9 repunit primes. 9. n. −. 1. =. (. 3. n. +. 1. ). (. 3. n. −. 1. ). {\ ... Base 4 repunit primes[edit]. The only base 4 repunit prime is 5 (. 11. 4. {\displaystyle 11_{4}}. ). 4. n. −. 1. =. (. 2. n. + ... 5, 13, 131, 149, 1699, ... (sequence A004063 in the OEIS).. Base 8 repunit primes[edit]. The only base 8 repunit prime is 73 ( ...

https://en.wikipedia.org/wiki/Repunit

... of which the first few bases are sequenced, yielding several millions of "reads", each 30 to 500 base pairs ("DNA characters") ... BWT for Sequence Prediction *BWT has also been proved to be useful on sequence prediction which is a common area of study in ... BWT for Sequence Alignment *The advent of next-generation sequencing (NGS) techniques at the end of the 2000s decade has led to ... "Succinct BWT-Based Sequence Prediction". Database and Expert Systems Applications: Lecture Notes in Computer Science. 11707 (10 ...

https://en.wikipedia.org/wiki/Burrows–Wheeler_transform

A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different ... Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical ... Croux C, Monchois V, Willemot RM, Remaud-simeon M, Monsan P (1996). "Cloning and sequencing of a gene coding for a novel ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_70

Bibcode:2011arXiv1110.3836G. Sloane, N. J. A. (ed.). "Sequence A161872 (Smallest unhappy number in base n)". The On-Line ... Are base 2 and base 4 the only bases that are happy? (more unsolved problems in mathematics) A happy base is a number base b {\ ... as base 2 and base 4 are happy bases. In base 6, the 6-happy primes below 1296 = 64 are 211, 1021, 1335, 2011, 2425, 2555, 3351 ... The only happy bases less than 5×108 are base 2 and base 4. For b = 4 {\displaystyle b=4} , the only positive perfect digital ...

https://en.wikipedia.org/wiki/Happy_number

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_108

A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different ... Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical ... Igarashi T, Yamamoto A, Goto N (1995). "Sequence analysis of the Streptococcus mutans Ingbritt dexA gene encoding extracellular ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_66

A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different ... Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical ... This domain is situated at the base of the catalytic domain, however its function remains unknown. The central domain is the ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_65

The tone sequence is based on just intonation; a good player can produce a wide tonal range. The sound of the lurs is powerful ...

https://en.wikipedia.org/wiki/Brudevælte_Lurs

A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different ... Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical ... Rothe B, Rothe B, Roggentin P, Schauer R (April 1991). "The sialidase gene from Clostridium septicum: cloning, sequencing, ... expression in Escherichia coli and identification of conserved sequences in sialidases and other proteins". Molecular & General ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_33

Courts these days are making policy-based decisions, untethered from any rule of law, aimed at killing patents they don't like. ... So they wanted to focus on genetic fragments containing paternally inherited sequences the mother did not share, but had ... mc2 and based on a requirement to keep speculator trolls out: [I]f the breadth of the claim is sufficiently limited to a ...

https://en.wikipedia.org/wiki/Ariosa_v._Sequenom

The Vistula estuary was settled by Slavs in the 7th and 8th century.[26] Based on archeological and linguistic findings, it has ... "Record of the Vistula ice lobe advances in the Late Weichselian glacial sequence in north-central Poland". Quaternary ... and considerable predisposition of its older base. The asymmetry of the river basin (right-hand to left-hand side) is 73-27%. ...

https://en.wikipedia.org/wiki/Vistula

... base added to ketone, using weak or insoluble bases, e.g., NaOEt in EtOH, or NaH) provides the more-substituted thermodynamic ... Ozonolysis, and related dihydroxylation/oxidative sequences, cleave alkenes to give aldehydes or ketones, depending on alkene ... Acid/base properties of ketonesEdit. Ketones are far more acidic (pKa ≈ 20) than a regular alkane (pKa ≈ 50). This difference ... with either stoichiometric and catalytic base. Using very strong bases like lithium diisopropylamide (LDA, pKa of conjugate ...

https://en.m.wikipedia.org/wiki/Ketone

... based on morphological and DNA sequence comparisons, Chalara fraxinea was suggested to be the asexual stage (anamorph) of the ... The sequence has been published on the website OpenAshDieBack and offers clues to how the fungus infects trees. The study has ... 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 ...

https://en.wikipedia.org/wiki/Hymenoscyphus_pseudoalbidus

She then appeared in some movie shorts with sequences based on famous paintings. She received critical recognition for the 1921 ... On January 2, 1930, while filming sequences for the Fox movie Such Men Are Dangerous, Kenneth Hawks was killed in a mid-air ... but her small part in a dream sequence wound up on the cutting room floor. Paramount let her contract lapse. ...

https://en.wikipedia.org/wiki/Mary_Astor

Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10. Somat. Cell Mol. Genet. March 1993, 19 (2): ... PDB rendering based on 1ifr.. 有效结构. PDB. 直系同源检索：PDBe, RCSB ...

https://zh.wikipedia.org/wiki/LMNA

Family-pedigree based mapping[edit]. Family based QTL mapping, or Family-pedigree based mapping (Linkage and association ... 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 ... Using family-pedigree based approach has been discussed (Bink et al. 2008). Family-based linkage and association has been ...

https://en.wikipedia.org/wiki/Polygenic_inheritance

The two major types, are silicate based and carbonate based. The majority of silica cements are composed of quartz but can ... Thick sequences of sedimentary (colluvial) breccias are generally formed next to fault scarps in grabens. ... Classification schemes for mudrocks tend to vary but most are based on the grain size of the major constituents. In mudrocks, ... However, others have used the term shale to further divide mudrocks based on the percentage of clay constituents. The plate- ...

https://en.m.wikipedia.org/wiki/Clastic_rock

... (formerly known as Ingenuity Systems, Inc) is a company based in Redwood City, California, USA, to ... Laboratory Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing ... All QIAGEN Silicon Valley use the Ingenuity Knowledge Base, which contains biological and chemical interactions and functional ... BD Cell Pathways "Ingenuity Systems Announces Immediate Availability Of The Ingenuity Pathways Knowledge Base" (Press release ...

https://en.wikipedia.org/wiki/QIAGEN_Silicon_Valley

Rossini's opera La gazza ladra and The Adventures of Tintin comic The Castafiore Emerald are based on this theme. However, one ... An analysis of mitochondrial DNA sequences published in 2003 confirmed that the black-billed magpie and the yellow-billed ... Union decided to treat the black-billed magpie as a separate species based on studies of the vocalization and behaviour that ...

https://en.m.wikipedia.org/wiki/Eurasian_magpie

Minimum magnitude sequence. (1, 4, 4, 4, 4, and 4 goes on for the rest) -- Positive sequence. Multiply the right most digit by ... For example, in base 10, the factors of 101 include 2, 5, and 10. Therefore, divisibility by 2, 5, and 10 only depend on ... Positive sequence Multiply the right most digit by the left most digit in the sequence and multiply the second right most digit ... Minimum magnitude sequence (1, 3, 2, 6, 4, 5, cycle repeats for the next six digits) Period: 6 digits. Recurring numbers: 1, 3 ...

https://en.wikipedia.org/wiki/Divisibility_rule

The Animatrix (2003, animated sequence). *Hajime no Ippo: Mashiba vs. Kimura (2003) ... Anime series based on manga. *Animated television series about cats. *Comedy anime and manga ...

https://en.wikipedia.org/wiki/Chi's_Sweet_Home

... the attack-point sequence of the two measures is reversed. Most salsa is in 2-3 clave and most salsa piano guajeos are based on ... The following guajeo is based on the clave motif in a 2-3 sequence. The cinquillo rhythm is now in the second measure. ... 8 clave-based music is generated from cross-rhythm, it is possible to count or feel the 6. 8 clave in several different ways. ... The following afrobeat guitar part is a variant of the 2-3 onbeat/offbeat motif.[83] Even the melodic contour is guajeo-based. ...

https://en.wikipedia.org/wiki/Clave_(rhythm)

The genome of S. pneumoniae is a closed, circular DNA structure that contains between 2.0 and 2.1 million base pairs depending ... The recent advances in next-generation sequencing and comparative genomics have enabled the development of robust and reliable ... S. pneumoniae can also be distinguished based on its sensitivity to lysis by bile, the so-called "bile solubility test". The ... For instance, the Xisco gene was recently described as a biomarker for PCR-based detection of S. pneumoniae and differentiation ...

https://en.wikipedia.org/wiki/S._pneumoniae

What is accepted as the standard form today in both West Bengal and Bangladesh is based on the West-Central dialect of Nadia ... There is yet to be a uniform standard collating sequence (sorting order of graphemes to be used in dictionaries, indices, ... The modern literary form of Bengali was developed during the 19th and early 20th centuries based on the dialect spoken in the ... In spite of some modifications in the 19th century, the Bengali spelling system continues to be based on the one used for ...

https://en.wikipedia.org/wiki/Bengali_language

Pyykkö, Pekka (2011). "A suggested periodic table up to Z ≤ 172, based on Dirac-Fock calculations on atoms and ions". Physical ... to this debate on the basis of moving to a 32-column table and consideration of which option results in a continuous sequence ... Exclusion of all elements is based on properties of earlier actinides, which show a much wider variety of chemistry (for ...

https://en.m.wikipedia.org/wiki/Group_3_element

Statistical, likelihood-based approaches: Statistical, likelihood-based [37][38] iterative expectation-maximization algorithms ... Because the two scans can be performed in immediate sequence during the same session, with the patient not changing position ... based regularization in a wavelet or other domain), such as via Ulf Grenander's Sieve estimator[41][42] or via Bayes penalty ... Neurology: PET neuroimaging is based on an assumption that areas of high radioactivity are associated with brain activity. What ...

https://en.m.wikipedia.org/wiki/PET_scan

More than one main vein (nerve) at the base. Lateral secondary veins branching from a point above the base of the leaf. Usually ... 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/ ... BaseEdit. Acuminate. Coming to a sharp, narrow, prolonged point.. Acute. Coming to a sharp, but not prolonged point.. ... When the leaf base completely surrounds the stem, the leaves are said to be perfoliate, such as in Eupatorium perfoliatum. ...

https://en.m.wikipedia.org/wiki/Cauline

Genome-sequencing showed that this outbreak was not related to the 2014-15 West Africa Ebola virus outbreak, but was the same ... Developments in organ-on-a-chip technology have led to a chip-based model for Ebola haemorrhagic syndrome.[262] ... 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 ...

https://en.m.wikipedia.org/wiki/Ebola_virus_disease

The clinical diagnosis must be based on the presence of one or more of the symptoms listed below, because the syndrome itself ... The CRH test uses recombinant human or bovine-sequence CRH, which is administered via a 100μg intravenous bolus dose. The ... A population-based study". Journal of Clinical Endocrinology and Metabolism. 86 (1): 117-123. doi:10.1210/jcem.86.1.7093. PMID ... Aidan Carney and based on statistical evidence, was that the basophil adenoma Minnie might have harbored underwent partial ...

https://en.m.wikipedia.org/wiki/Cushing's_disease

... residue in the sequence Asn-X-Ser or Asn-X-Thr where X is any amino acid except proline. This sequence is called a ... Marquardt T, Denecke J (June 2003). "Congenital disorders of glycosylation: review of their molecular bases, clinical ... The high sequence similarity between the prokaryotic and the eukaryotic STT3 suggests that their structures are similar. ...

https://en.wikipedia.org/wiki/Oligosaccharyltransferase

Henceforth, batteries were designated in a single alphabetical sequence in order of seniority from date of formation[24] and ... it has been based in England, initially at Aldershot but latterly at Colchester.[61] ... currently based in Merville Barracks in Colchester. ...

https://en.wikipedia.org/wiki/I_Parachute_Battery_

A sequence of two high-profile studies by a team from the Massachusetts Institute of Technology and the Harvard School of ... Similarly, if a child lives with someone other than a parent, he may still be eligible based on its individual status.[74] ... Unlike Medicare, Medicaid is a means-tested, needs-based social welfare or social protection program rather than a social ... The Low-Income Wage Rate: State welfare programs base the level of assistance they provide on some concept of what is minimally ...

https://en.wikipedia.org/wiki/Medicaid

The mallard is omnivorous and very flexible in its choice of food.[61] Its diet may vary based on several factors, including ... Mitochondrial DNA data for the D-loop sequence suggests that mallards may have evolved in the general area of Siberia. Mallard ... The genome of Anas platyrhynchos was sequenced in 2013.[6] ...

https://en.m.wikipedia.org/wiki/Mallard

"Sex-Based Roles Gave Modern Humans an Edge, Study Says". National Geographic News. Retrieved 2008-02-03.. ... "Callaway, Ewen (22 September 2011), "First Aboriginal genome sequenced", Nature, Nature News, doi:10.1038/news.2011.551 ... An artist's rendering of a temporary wood house, based on evidence found at Terra Amata (in Nice, France) and dated to the ... In general, their actual diet in the wild is about 95% plant-based, with the remaining 5% filled with insects, eggs, and baby ...

https://en.wikipedia.org/wiki/Paleolithic

Over time, base changes in the DNA sequence can arise from deamination mutations. When adenine is deaminated, it becomes ... Hypoxanthine can bind to cytosine, and when the XC base pair is replicated, it becomes a GC (thus, an A → G base change).[20] ... Its existence was first proven in 1962,[4] and first sequenced in 1986-when two Japanese research teams sequenced the ... both very common in chloroplast transit sequences-making up 20-30% of the sequence)[45] are often the amino acids that accept ...

https://en.m.wikipedia.org/wiki/Chloroplast_DNA

... a base-emitter junction and a base-collector junction, separated by a thin region of semiconductor known as the base region. ( ... A 3-digit sequence number (or one letter then two digits, for industrial types) follows. With early devices this indicated the ... Also, as the base-emitter voltage (VBE) is increased the base-emitter current and hence the collector-emitter current (ICE) ... A bipolar transistor has terminals labeled base, collector, and emitter. A small current at the base terminal (that is, flowing ...

https://en.wikipedia.org/wiki/Discrete_transistor

... vulgaris is diagnosed based on a medical professional's clinical judgment.[15] The evaluation of a person with suspected ... scientists reported the first genome sequencing of a C. acnes bacteriophage (PA6). The authors proposed applying this research ... June 2012). "Topical antimicrobial treatment of acne vulgaris: an evidence-based review". American Journal of Clinical ... Levy LL, Zeichner JA (October 2012). "Management of acne scarring, part II: a comparative review of non-laser-based, minimally ...

https://en.wikipedia.org/wiki/Acne_vulgaris

Flats Sequencing System. *Locatable Address Conversion System. *United States Postal Savings System ... Information-Based Indicia. *The Inspectors. *Intelligent Mail barcode. *Label 228. *List of postal killings ...

https://en.wikipedia.org/wiki/Template:United_States_Postal_Service

Huston JP, Hasenöhrl RU, Boix F, Gerhardt P, Schwarting RK (1993). "Sequence-specific effects of neurokinin substance P on ... the peptide based NK1RA) against cisplatin-induced emesis in the ferret.[75] It is likely that some peripheral exposure ... The deduced amino acid sequence of substance P is as follows:[3] ...

https://en.m.wikipedia.org/wiki/Substance_P

Nanopore Sequencing to Identify DNA Bases. A British company has demonstrated an important step for a new sequencing technique. ...

https://www.technologyreview.com/2009/02/24/215401/nanopore-sequencing-to-identify-dna-bases/

In fact, I had a client this morning that needed to convert a DVCPro-50 16:9 sequence into a DV 4:3 video. Heres how to do it. ... 4) The movie will export - and will take a while to do so, depending upon the length of the sequence you are exporting. Use ... I just wanted to mention a minor problem I discovered with your "converting a 16:9 sequence to 4:3 video" article. I was ... Slade Knowledge Base is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, 2018 ...

https://www.ucl.ac.uk/slade/know/3305

Local alignment of two-base encoded DNA sequence ... Multiple DNA and protein sequence alignment based on segment-to ... Whole methylome analysis by ultra-deep sequencing using two-base encoding by Christina A. Bormann Chung, Victoria L. Boyd, ... Insertion sequences by Jacques Mahillon, Michael Ch, Jacques Mahillon, Michael Chandler - Microbiol Mol. Biol. Rev , 1998 ... Local Alignments of DNA Sequences by unknown authors , 2002 "... Abstract This paper presents aheuristic for finding close to ...

https://citeseerx.ist.psu.edu/search?q=Local+alignment+of+two-base+encoded+DNA+sequence

MOABS: model based analysis of bisulfite sequencing data.. Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W ... e) and (f) Same as (c) and (d) with 4X sequencing depth by random sampling. The 10000 times of random shuffle of TFBSs ... Sequencing depth is randomly sampled from 5-fold to 50-fold. The Y-axis shows the percentage of true DMCs predicted at 5% FDR. ... Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the ...

https://www.ncbi.nlm.nih.gov/pubmed/24565500

... Published 7:30 AM ET Thu, 1 Oct 2015 Globe ... These forward-looking statements are based upon managements current expectations, are subject to known and unknown risks, and ... HTG EdgeSeq Immuno-Oncology Assay couples HTGs proprietary nuclease protection chemistry with next-generation sequencing (NGS ... system capabilities have been expanded to fully automate sample and targeted library preparation for next-generation sequencing ...

https://www.cnbc.com/2015/10/01/globe-newswire-htg-molecular-launches-next-generation-sequencing-based-immuno-oncology-assay.html

Journal of Integer Sequences, Vol. 10 (2007), Article 07.1.8. Sequences of Generalized Happy Numbers with Small Bases H. G. ... For bases b ≤ 5 and exponents e ≥ 2, there exist arbitrarily long finite sequences of d-consecutive e-power b-happy numbers for ... Published in Journal of Integer Sequences January 8 2007. Return to Journal of Integer Sequences home page ... Concerned with sequence A000108 .) Received June 29 2006; revised version received January 8 2007. ...

http://www.emis.de/journals/JIS/VOL10/Grundman/grundman5.html

"Analysis of similarity/dissimilarity of DNA sequences based on nonoverlapping triplets of nucleotide bases," Journal of ... Numerical Characterization of DNA Sequence Based on Dinucleotides. Xingqin Qi,1 Edgar Fuller,2 Qin Wu,3 and Cun-Quan Zhang2 ... Z. H. Qi and X. Q. Qi, "Numerical characterization of DNA sequences based on digital signal method," Computers in Biology and ... B. Liao, R. Li, W. Zhu, and X. Xiang, "On the similarity of DNA primary sequences based on 5-D representation," Journal of ...

https://www.hindawi.com/journals/tswj/2012/104269/ref/

... and application of deep learning model architectures for any biological sequence data. We demonstrate on DNA sequences how ... a PyTorch-based deep learning library for fast and easy development, training, ... and the evaluation of these new models on biological sequence data. ... Selene: a PyTorch-based deep learning library for sequence data. *Kathleen M. Chen ORCID: orcid.org/0000-0002-7461-95301 na1, ...

https://www.nature.com/articles/s41592-019-0360-8?error=cookies_not_supported&code=ada176a6-58c8-4153-ae47-2c61ca0b6bce

Sequence Cut Site Overhang Properties (NEB Enzymes Only) Nb ... Enzyme Finder - Sequence , 6 Bases. Enzyme. Sequence. Cut Site ... Home Tools & Resources Selection Charts Enzyme Finder - Sequence , 6 Bases ... DNA Library Prep Kit with novel fragmentation reagent meets the dual challenge of generating high quality next gen sequencing ... DNA Library Prep Kit with novel fragmentation reagent meets the dual challenge of generating high quality next gen sequencing ...

https://www.neb.com/tools-and-resources/selection-charts/enzyme-finder---sequence-6-bases

... hz5 at njit.edu hz5 at njit.edu Tue Jun 11 13:35:46 EDT 2002 *Previous message (by ... I am hoping that your collective brains can help me find a web based , software suite to do some simple DNA sequence ... We will complete the class by cloning and sequenceing a gene, , and , we would like to do some sequence analysis with the ... Simply , looking at the sequence, translation, rev/comp sorts of things. , However, , we dont really want to install software ...

http://bioinformatics.org/pipermail/bbb/2002-June/000729.html

... sequence_base::_M_swap (_Safe_sequence_base &__x) [protected] Swap this sequence with the given sequence. This operation also ... gnu_debug::_Safe_sequence_base::~_Safe_sequence_base () [inline, protected] Notify all iterators that reference this sequence ... gnu_debug::_Safe_sequence_base - SYNOPSIS. Inherited by __gnu_debug::_Safe_sequence, _Sequence ,, __gnu_debug::_Safe_sequence, ... sequence, _Sequence ,::_M_transfer_iter(). _Safe_iterator_base* __gnu_debug::_Safe_sequence_base::_M_iterators The list of ...

http://manpages.ubuntu.com/manpages/precise/man3/__gnu_debug__Safe_sequence_base.3cxx.html

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.. Albrecht M1, Sharma CM, Reinhardt R, Vogel J, ... A) Calculated sequence graphs for C. trachomatis cryptic plasmid. Graphs show the number of sequence reads for every nucleotide ... Shown are relative numbers of groups of sequence length in relation to the total number of reads per library. (B) Sequence read ... We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. ...

https://www.ncbi.nlm.nih.gov/pubmed/19923228?dopt=Abstract

Modeling and automation of sequencing-based characterization of RNA structure. Sharon Aviran, Cole Trapnell, Julius B. Lucks, ... Modeling and automation of sequencing-based characterization of RNA structure. Sharon Aviran, Cole Trapnell, Julius B. Lucks, ... Modeling and automation of sequencing-based characterization of RNA structure. Sharon Aviran, Cole Trapnell, Julius B. Lucks, ... Modeling and automation of sequencing-based characterization of RNA structure Message Subject (Your Name) has sent you a ...

https://www.pnas.org/content/108/27/11069.full

In this paper,we present a new gait recognition scheme based on multi-view... ... Wang Y., Yu S., Wang Y., Tan T. (2005) Gait Recognition Based on Fusion of Multi-view Gait Sequences. In: Zhang D., Jain A.K. ( ... In this paper,we present a new gait recognition scheme based on multi-view gait sequence fusion. An experimental comparison of ... On the other hand, we also find that fusion of gait sequences with an angle difference greater than or equal to 90° can achieve ...

https://link.springer.com/chapter/10.1007/11608288_80

Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. ... 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 ... Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. ...

https://link.springer.com/chapter/10.1007/978-3-642-28839-5_25

New frames in an image sequence (video) are segmented based on the prior segmentati ... We describe an algorithm for context-based segmentation of visual data. ...

http://ieeexplore.ieee.org/document/1580490/keywords?reload=true

... Shadi A. Issa,1 Romeo Kienzler,2 Mohamed El-Kalioby,1 Peter ... Majid Hajibaba, Saed Gorgin, and Mohsen Sharifi, "Sequence similarity parallelization over heterogeneous computer clusters ... "Optimization of data-intensive workflows in stream-based data processing models," Journal of Supercomputing, vol. 73, no. 9, pp ... "Data-intensive workflow optimization based on application task graph partitioning in heterogeneous computing systems," ...

https://www.hindawi.com/journals/bmri/2013/791051/citations/

Have you tried doing a script for checking if there is a missing file based on the sequence number? Im tried doing it but I ... Have you tried doing a script for checking if there is a missing file based on the sequence number? Im tried doing it but I ... save the previous sequence number lcnt=seqno } input > output ... Solved] Move Files based on Filename time. *› i want to find ...

https://www.computing.net/answers/unix/checking-missing-file-based-on-sequence-number/9110.html

Citation: P, P., J, P., and Palanisamy, K., "Optimization of Proving Ground Durability Test Sequence Based on Relative Damage ... Optimization of Proving Ground Durability Test Sequence Based on Relative Damage Spectrum 2018-01-0101. ... Hence the PG test sequence must be optimal enough such that it includes all the range of frequencies representing the actual ... PG validation requires a specific durability test sequence for every segment of commercial vehicles due to different customer ...

https://www.sae.org/publications/technical-papers/content/2018-01-0101/

... a series of nine research projects that will use next-generation sequencing to address specific research questions that until ... Cancer Research UK Launches Nine Sequencing-Based Genomics Projects Nov 30, 2011 ... Chris Jones, also at the Institute of Cancer Research in London, will sequence pediatric diffuse intrinsic pontine glioma. ... Dominique Bonnet from Cancer Research UKs London Research Institute will perform next-generation sequencing of leukemic stem ...

https://www.genomeweb.com/sequencing/cancer-research-uk-launches-nine-sequencing-based-cancer-projects

... aim to develop tests based on several platforms, including the Ion Torrent PGM and Illumina HiSeq. ... A new program funded by the UK government aims to bring sequencing-based cancer tests to the market as part of a broad ... UK Government Funding Development of Sequencing-Based Cancer Tests. Jun 21, 2011 ... Exosome-Based Treatment Targeting KRAS G12D-Mutated Pancreatic Cancer to Enter Human Studies Next Month. Premium ...

https://www.genomeweb.com/sequencing/uk-government-funding-development-sequencing-based-cancer-tests

Gene sequence-based diversity in Pisum:. Alignments were generated for each of the 39 gene segment sequence sets. Nucleotide ... Sequence-based diversity trees:. To investigate the tree structure of the complete sequence set, the aligned gene-derived ... 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, ...

https://www.genetics.org/content/177/4/2263

This has led to considerable interest in PCR-based markers, in particular those based on simple sequence repeats (SSR). ... A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database ... Sequence checking and primer design: The systematic checking of the sequences, against an in-house database of SSR-containing ... SSR isolation and characterization: SSR-containing DNA sequences were derived from public access sequence databases and from ...

https://www.genetics.org/node/330337.full.print

File activerecord/lib/active_record/base.rb, line 672 def set_sequence_name(value = nil, &block) define_attr_method :sequence_ ... class Project , ActiveRecord::Base set_sequence_name projectseq # default would have been project_seq end. ... set_sequence_name(value = nil, &block). public Sets the name of the sequence to use when generating ids to the given value, or ... If a sequence name is not explicitly set when using PostgreSQL, it will discover the sequence corresponding to your primary key ...

https://apidock.com/rails/v3.0.9/ActiveRecord/Base/set_sequence_name/class

Here, we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor ... The sequence-based genotyping method used here has limitations caused by the lack of a plum reference assembly and the reliance ... In the present study, we generated a set of sequence-based SNP markers densely distributed across the Prunus genome in order to ... Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping. *Tetyana Zhebentyayeva ...

https://www.nature.com/articles/s41438-018-0090-6?error=cookies_not_supported&code=97eabbbd-2474-4d13-a0ca-84f2319abfb0

We present the notion of a similarity query and we review similarity measures proposed so far for sets and sequences. We ... We introduce a new similarity measure that can be successfully used with sequences. We present algorithms for efficient ... Attributes containing sets or sequences of elements appear in various application domains, e.g. in telecommunication and retail ... Currently available database systems support neither indexing nor advanced querying of attributes containing sets or sequences ...

http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.6526

Sequence-based bioinformatics. The analysis of DNA, RNA and protein sequences is traditionally one of the major application ... Such analyses require methods for sequence alignment, phylogenetics reconstruction (for functional analysis), elucidation of ... a pressing need for novel bioinformatics methods that can infer biological functions and processes directly from sequence-level ...

https://www.nbic.nl/research/research-projects/sequence-based-bioinformatics/index.html

... ability to detect piconewton scale forces in order to read off sequencing information based on the interaction of nucleotides ... Many new sequencing technologies are being developed to achieve these goals. Our technique takes advantage of the atomic force ... We have successfully completed two of the major pieces needed to sequence DNA with an AFM. The problem of nonspecific adhesion ... The desire to sequence DNA is fueled by the knowledge that the information locked inside of genomes can help fields as varied ...

http://www.nsti.org/Nanotech2006/showabstract.html?absno=864

sequor: A sequence labeler based on Collinss sequence perceptron.. [ bsd3, library, natural-language-processing, program ] [ ... array (,=0.2), base (,=3 && ,5), binary (,=0.5), bytestring (,=0.9.2), containers (,=0.2), mtl (,=1.1), nlp-scores (,=0.6.0), ...

http://hackage.haskell.org/package/sequor

sequor: A sequence labeler based on Collinss sequence perceptron. The sequor package. [ Tags: bsd3, library, natural-language- ... sequor 0.2.2 AUTHOR: Grzegorz Chrupała ,[email protected], Sequor is a sequence labeler based on Collinss sequence ... If passed a sequence they are applied to each of its elements. For example (Suffix 3 (Row 0)) will return the sequence of ... array (,=0.2), base (,=3 && ,5), binary (,=0.5), bytestring (,=0.9), containers (,=0.2), mtl (,=1.1), pretty (,=1.0), text (,= ...

http://hackage.haskell.org/package/sequor-0.2.3

John Neoptolemos from the University of Liverpool will conduct whole-genome sequencing of pancreatic cancers from patients selected from the European Study Group for Pancreatic Cancer trials to identify novel pathways and networks determining response to chemotherapy and chemoradiotherapy. (genomeweb.com)
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)
While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. (sigmaaldrich.com)

Further characterization is necessary for those isolates that have identical 16S sequences and can be done using SLST or MLST. (criver.com)
Robinson K, Schreier H. Isolation, sequence and characterization of the maltose-regulated mlrA gene from the hyperthermophilic archaeum Pyrococcus furiosus. (labome.org)
Next-generation sequencing has aided characterization of genomic variation. (sigmaaldrich.com)

Automated on the HTG EdgeSeq system, HTG EdgeSeq Immuno-Oncology Assay couples HTG's proprietary nuclease protection chemistry with next-generation sequencing (NGS). (cnbc.com)
Our new technology, software, and chemistry overcome this bottleneck and give sequence reads that are typically twice as long as those from previous PyroMark systems. (qiagen.com)
p. 934 , published online 26 April) developed a 5hmC sequencing chemistry that selectively oxidizes 5hmC to 5-formylcytosine and then to uracil while leaving 5mC unchanged. (sciencemag.org)
Combining synthetic polymers with protein-inspired chemistry and DNA sequences allows the formation of soft gels, held together by DNA base pairing and disulfide links, which in turn allow recognition of DNA or RNA sequences and an amplified response as the gel swells. (nottingham.ac.uk)
To date the most reliable method of determining a genetic sequence is through the use of the Sanger chain termination chemistry, however a typical mammalian sequence costs millions of dollars and requires many months for completion. (nsti.org)
A Study of Specific Pair Bonding of Nucleic Acid Bases by Ultra-Red Spectroscopy" (in Japanese), Yoshimasa Kyogoku, The Field of Chemistry, vol. 22, No. 4, pp. 364-374 (1968). (freepatentsonline.com)
The prior art DNA base sequencing is a wet chemistry technique consisting principally of DNA length separation making use of electrophoresis. (freepatentsonline.com)

Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. (psu.edu)
Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. (nih.gov)
The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen. (nih.gov)
Such analyses require methods for sequence alignment, phylogenetics reconstruction (for functional analysis), elucidation of genome structures, functional analysis of non-coding DNA, expression analysis, and determining genetic variation. (nbic.nl)
Its genome has been sequenced but little is known about the occurrence and distribution of small non-coding RNAs in this biotechnologically relevant organism. (nih.gov)
Base-calling on the major alone yields accuracy commensurate with single sequence approaches, and joint base-calling provides results for the minor which, while being of lesser quality, incurs no additional cost and can be ultimately used in the genome assembly process. (mit.edu)
Increased discrimination at the strain level can be achieved by sequencing, analyzing and comparing highly variable loci (regions) in the organism's genome. (criver.com)
Manassas, VA - October 1, 2019 - ATCC launched its new ATCC Genome Portal , a publicly available database of reference-quality genome sequences matched to authenticated ATCC biological materials that will help researchers interpret and reproduce their results with confidence. (atcc.org)
The portal, which launched with an initial 250 genome sequences of widely used bacterial strains, delivers on ATCC's Enhanced Authentication Initiative , a component of the first of five core pledges under the Incredible 2020 Initiative aimed at increasing reproducibility in biological research. (atcc.org)
This problem is exacerbated by the absence of standardized methods for developing and validating reference-quality genome sequences. (atcc.org)
Through our Enhanced Authentication Initiative, we have identified the key challenges with existing publicly available data and have developed a solution for improving the quality of reference genome sequences. (atcc.org)
Researchers can download high-quality genome sequences for use in bioinformatic analyses, view annotated data, and search for genomes using their own data. (atcc.org)
Methylation of the cytosine base in eukaryotic DNA (5mC) is an important epigenetic mark involved in gene silencing and genome stability. (sciencemag.org)
Nanopore-based methods have come under intense investigation recently due to the promise of inexpensive ultra high-throughput sequencing of DNA, with an entire mammalian sequence being determined at a cost of under $1,000 (goal set forth by the National Human Genome Research Institute located at http://www.genome.gov). (nsti.org)

Visual motion is one of the most important cues for the interpretation of image sequences. (bl.uk)
Research interest has naturally focused on the development of techniques that enable arbitrary image sequences to be efficiently decomposed into their constituent layers. (bl.uk)

How to subset sequences in fasta file based on sequence ID or Name? (stackoverflow.com)

A. Nandy, "A new graphical representation and analysis of DNA sequence structure: I. Methodology and Application to Globin Genes," Current Science , vol. 66, pp. 309-314, 1994. (hindawi.com)
Furthermore, the genomic compartment in which the markers reside might affect the diversity pattern seen, and it is possible that markers residing mainly in junk DNA might produce different results from markers based upon genes, which are predominantly euchromatic. (genetics.org)
Like our AccuGENX-ID ® methods for identification of bacteria and fungi using the 16S and ITS2 genes, our AccuGENX-ST ® sequence typing uses standard molecular biological methods of DNA extraction, PCR amplification and DNA sequencing of protein coding target genes to characterize your isolates to the strain level. (criver.com)
MLST and SLST analyze essential protein coding genes, or housekeeping genes, that encode for proteins necessary for the normal cellular functions of the bacterium all of which contain more variability in their sequences. (criver.com)
The target genes are PCR amplified using the gene-specific primers and subjected to comparative DNA sequence analysis. (criver.com)
Both the NGS platform and Oncomine reagents leverage the Ion AmpliSeq technology, which enables simultaneous sequencing of hundreds of genes, with high reproducibility and rapid turnaround time. (businesswire.com)
Employing the topological features in the protein interaction network and the sequence properties, we have built a machine learning classifier capable of predicting essential genes . (rsc.org)
in Escherichia coli, for example, the sequence is AGGAGGU, while the shorter GAGG dominates in E. coli virus T4 early genes. (wikipedia.org)

The code you're using is for a FASTA file that has blank lines between the sequences. (stackoverflow.com)
I have set of EST sequences in fasta file. (stackoverflow.com)

MOABS: model based analysis of bisulfite sequencing data. (nih.gov)
we would like to do some sequence analysis with the students. (bioinformatics.org)
We describe a fully automated data analysis pipeline for SHAPE-Seq analysis that includes read processing, mapping, and structural inference based on a model of the experiment. (pnas.org)
Our approach is inspired by probabilistic models used in RNA sequencing (RNA-Seq) analysis to measure transcript identity and abundance ( 8 ) and should be easily generalizable to any chemical probing technique that characterizes different aspects of RNA structure. (pnas.org)
In this paper, we present Exon, a user-friendly solution containing tools for online analysis of DNA sequences through compression based profiles. (springer.com)
Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. (genetics.org)
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 analysis of DNA, RNA and protein sequences is traditionally one of the major application areas for bioinformatics tools and methods. (nbic.nl)
Is the Subject Area "DNA sequence analysis" applicable to this article? (plos.org)
Combined with its uniquely low DNA and RNA sample input requirements from Formalin-Fixed Paraffin-Embedded (FFPE) tissues (as little as 10ng extracted nucleic acid per reaction), the Ion Torrent-based sequencing platform and reagents offer comprehensive sequence analysis of a wider variety of tumor samples, including limited or compromised specimens derived from FFPE tissue or fine needle aspirates. (businesswire.com)
DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. (softpile.com)
The real-time, high-resolution sequence output makes the technology highly suitable for applications including complex mutation analysis, microbial identification, and DNA methylation quantification. (qiagen.com)
Based on application, the NGS-based RNA sequencing market is segmented into expression profiling analysis, small RNA sequencing, De Novo transcriptome assembly, and variant calling & transcriptome epigenetics. (marketsandmarkets.com)
Furthermore, based on restriction enzyme analysis, it was found in 1991 that the region amplified with these primers was somewhat heterogeneous ( 15 ). (asm.org)
We have developed a computational tool, rVISTA, for high-throughput discovery of cis-regulatory elements that combines transcription factor binding site prediction and the analysis of inter-species sequence conservation. (unt.edu)
The exploitation of orthologous human-mouse data set resulted in the elimination of 95 percent of the 38,000 binding sites predicted upon analysis of the human sequence alone, while it identified 87 percent of the experimentally verified binding sites in this region. (unt.edu)

Sequence census methods reduce molecular measurements such as transcript abundance and protein-nucleic acid interactions to counting problems via DNA sequencing. (pnas.org)
Attributes containing sets or sequences of elements appear in various application domains, e.g. in telecommunication and retail databases, multimedia systems, web server logs, genetic and molecular databases, etc. (psu.edu)
The desire to sequence DNA is fueled by the knowledge that the information locked inside of genomes can help fields as varied as molecular medicine, bioarcheology, forensics, and environmental science. (nsti.org)
HaloPlex HS is a high-sensitivity, amplicon-based targeted sequencing method that incorporates molecular barcodes in the DNA library. (agilent.com)
Therefore, much works have focused on designing the DNA sequences to archive a reliable molecular computation and many algorithms have been proposed to obtain a set of good DNA sequences. (actapress.com)
Based on technology, the NGS-based RNA-sequencing industry is segmented into sequencing by synthesis, ion semiconductor sequencing, single molecular real-time sequencing, and nanopore sequencing. (marketsandmarkets.com)
For some taxonomic groups, advances in molecular sequencing have made it increasingly possible to observe and examine organisms and ecological communities using DNA-based sequences alone. (gbif.org)
Advances in molecular biology in the second half of the 20th century firmly established DNA sequence as the molecular substrate of inheritance ( 1 ). (sciencemag.org)
Terminal-sequence studies of high-molecular-weight ribonucleic acid. (wikipedia.org)

In order to access their genetic diversity and perform phylogenetic and demographic analyses, we captured and sequenced ~2,300 Ultra Conserved Elements. (usp.br)
In this paper, we show that taxonomic designations in Reticulitermes from California (USA) suggested in light of diVerences among CHC phenotypes are corroborated by phylogenetic analyses using mtDNA sequences. (usda.gov)

Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. (nih.gov)
If the 16S sequence is different, you can be sure that the isolates are different strains. (criver.com)
Since then, sequencing has shown the presence of several mutations in the few available clinical strains compared to the sequence of the type strain M. genitalium G37 ( 13 ). (asm.org)
We determined the discriminatory index (DI), i.e., the likelihood that unrelated strains sampled from the test population would be placed into different typing groups ( 10 ), by sequencing specimens from unrelated patients. (asm.org)

Charles Swanton from Cancer Research UK's London Research Institute will study intra-tumor genetic heterogeneity in renal cell carcinoma through multi-region exome sequencing to inform biomarker discovery strategies. (genomeweb.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)
Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. (nih.gov)
The guidances provide recommendations for designing, developing, and validating tests that use the technology, called next generation sequencing (NGS), and will play an important role in the continued advancement of individualized, genetic-based medicine. (fda.gov)
The first guidance issued today, " Use of Public Human Genetic Variant Databases to Support Clinical Validity for Genetic and Genomic-Based In Vitro Diagnostics ," describes an approach where test developers may rely on clinical evidence from FDA-recognized public databases to support clinical claims for their tests and help provide assurance of the accurate clinical evaluation of genomic test results. (fda.gov)
The second guidance issued today, " Considerations for Design, Development, and Analytical Validation of Next Generation Sequencing (NGS)-Based In Vitro Diagnostics (IVDs) Intended to Aid in the Diagnosis of Suspected Germline Diseases ," provides recommendations for designing, developing, and validating NGS-based tests used to diagnose individuals with suspected genetic diseases. (fda.gov)
In 2017, the FDA took several actions to streamline the development and review of a variety of genetic-based tests - authorizing a third-party option for conducting reviews NGS tumor profiling tests and making clearance recommendations to FDA , as well as outlining standardized development criteria for carrier screening tests to allow for their marketing without prior agency review. (fda.gov)

Agilent׷ amplicon-based technologies for target enrichment and amplification include HaloPlex / HaloPlex HS and SureMASTR. (agilent.com)
Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing. (sigmaaldrich.com)
Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. (sigmaaldrich.com)
We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. (sigmaaldrich.com)
All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. (sigmaaldrich.com)

Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. (genetics.org)
All the sequences from each gene target are aligned and compared to the other organisms' sequence data and the level of divergence or conservation between the organisms is calculated and displayed with a phylogenetic tree. (criver.com)
We will interpret the data for you and state whether the isolates are indistinguishable by the sequencing of the particular gene targets or whether the isolates are different sequence types. (criver.com)
In addition, we have also examined sequence properties such as open reading frame length, strand, and phyletic retention for their association with the gene essentiality. (rsc.org)
Gabel C, Maier R. Nucleotide sequence of the coxA gene encoding subunit I of cytochrome aa3 of Bradyrhizobium japonicum. (labome.org)
This clustering of base pair substitutions is unusual and suggests that mutation may result from unique structural features of the PKD1 gene. (labome.org)
A typing assay based on a diagnostic mgpB gene PCR was developed, evaluated, and applied directly to urogenital specimens. (asm.org)
The PCR can be based on the MgPa-1/MgPa-3 primer set located in conserved regions of the mgpB gene and producing an amplified fragment of 281 bp, as previously described ( 14 , 15 ). (asm.org)
The few available non-cluster-based methods only assess broad differences in gene expression between lineages, hence failing to pinpoint the exact types of divergence. (biorxiv.org)
We introduce a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of (i) within-lineage differential expression by detecting associations between gene expression and pseudotime over an entire lineage or by comparing gene expression between points/regions within the lineage and (ii) between-lineage differential expression by comparing gene expression between lineages over the entire lineages or at specific points/regions. (biorxiv.org)
We analyze a 680 base pair fragment of the mitochondrial DNA cytochrome oxidase (COII) gene from 45 new (21 collection localities) and two previously recorded samples of Reticulitermes from California using parsimony and maximum likelihood methods. (usda.gov)
We present a phylogenetic hypothesis for 40 species in the bird family Paridae, based on comparisons of nucleotide sequences of the mitochondrial cytochrome- b gene. (bioone.org)
Given the complementary relationship between rRNA and the Shine-Dalgarno sequence in mRNA, it was proposed that the sequence at the 3'-end of the rRNA determines the capacity of the prokaryotic ribosome to translate a particular gene in an mRNA. (wikipedia.org)

Our technique takes advantage of the atomic force microscope's (AFM) ability to detect piconewton scale forces in order to read off sequencing information based on the interaction of nucleotides with a cyclodextrin. (nsti.org)
The resulting product is treated with ExoSAP-IT™, prior to sequencing, to degrade the unincorporated primers and hydrolyze the free nucleotides. (thermofisher.com)
Nanopore sequencing technology registers the highest growth rate in the market as it is the only sequencing technology with direct RNA-sequencing capabilities and facilitates sequencing of full-length RNA strands and modified RNA nucleotides using a simple library prep, without the need of conversion to double-stranded DNA. (marketsandmarkets.com)
Obvious reasons for preferential realization of pairing phase 3 are the elevated GC content and the near equi- valent frequencies of base pairing nucleotides (A C25 U, C C25 G) at the third codon site, relative to other sites (Supplementary Table 1). (psu.edu)
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)
They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence AGGAGGU, which is found upstream of the start codon AUG in a number mRNAs found in viruses that affect E. coli. (wikipedia.org)

Sequencing of this bisulfite-treated DNA permits the detection of methylation at specific sites. (psu.edu)
We introduce oxidative bisulfite sequencing (oxBS-Seq), the first method for quantitative mapping of 5hmC in genomic DNA at single-nucleotide resolution. (sciencemag.org)

Published in Journal of Integer Sequences January 8 2007. (emis.de)

New DNA-based materials have been developed which can be programmed to respond to specific nucleic acid sequences, with potential applications in sensing and controlled release. (nottingham.ac.uk)

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. (nih.gov)
We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, respectively. (nih.gov)
Using deep sequencing we analyzed the transcriptome at the end of exponential growth, which corresponds to the onset of secondary metabolism. (nih.gov)

Using nanopore, bowtie, and bowtie-nanopore compound structures, probable application of the surface plasmon resonance (SPR) in DNA sequencing is investigated by employing the discrete dipole approximation method. (osapublishing.org)
The sequence of the DNA is determined via modulation of the electrical properties, as the strand translocates through the nanopore. (nsti.org)

In this approach, a modified deblocking filter is used for low to moderate motion video sequences. (go.jp)
The subjective and objective results are in conformity of the original H.264/AVC deblocking filter for low and moderate motion video sequences. (go.jp)

Different marker methods can give different views of diversity, depending upon the evolutionary parameters of the underlying DNA sequence variation. (genetics.org)
and transposon insertion-based marker methods should lie between these two, reflecting their intermediate mutation rate, although few studies have been carried out to test this. (genetics.org)
All this, combined with the limited availability or complete lack of other experimental data, creates a pressing need for novel bioinformatics methods that can infer biological functions and processes directly from sequence-level information. (nbic.nl)
s methods allows us to construct quaternary PCS/PZCS sets from binary PCS/PZCS sets with sub-sequences of arbitrary length. (aimsciences.org)
While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. (sigmaaldrich.com)

Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. (nih.gov)
The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. (nih.gov)
Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. (nih.gov)

The main building block for UNITE is the 'species hypothesis' (SH), which groups similar sequences into provisional species-level clusters. (gbif.org)
The identification of similar sequences in this report is based on clustering as described here . (rcsb.org)
In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff. (rcsb.org)

The Shine-Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. (wikipedia.org)
In 1973 Dalgarno and Shine proposed that in eukaryotes, the 3'-end of the small 18S rRNA may play a role in the termination of protein synthesis by complementary base pairing with termination codons. (wikipedia.org)
Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it was proposed to have a role in the termination of protein synthesis in eukaryotes. (wikipedia.org)

We focus on a novel assay utilizing this approach, called s elective 2′- h ydroxyl a cylation analyzed by p rimer e xtension sequencing (SHAPE-Seq), that can be used to characterize RNA secondary and tertiary structure. (pnas.org)
Here, we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor Eurasian plum species. (nature.com)

The mature proteins were 94% identical to each other and 36% identical to the sequences of bacterial L-arginine:inosamine phosphate amidinotransferases. (labome.org)
Many studies have confirmed that base pairing between the Shine-Dalgarno sequence in mRNA and the 3' end of 16S rRNA is of prime importance for initiation of translation by bacterial ribosomes. (wikipedia.org)

A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. (genetics.org)
This has led to considerable interest in PCR-based markers, in particular those based on simple sequence repeats (SSR). (genetics.org)

This approach allows a single electrophoresis experiment to process two sequences, using the same quantity of reagents and machine hours as for a single sequence. (mit.edu)

MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Binomial hierarchical model and is capable of processing two billion reads in 24 CPU hours. (nih.gov)
Dash curves indicate inferred methylation ratio Beta distributions from low (Sample #1) or high sequencing depth (Sample #2). (nih.gov)

In this paper,we present a new gait recognition scheme based on multi-view gait sequence fusion. (springer.com)
Sugie, Y., Kobayashi, T.: Media-integrated biometric person recognition based on the dempster-shafer theory. (springer.com)
Wang Y., Yu S., Wang Y., Tan T. (2005) Gait Recognition Based on Fusion of Multi-view Gait Sequences. (springer.com)
Digestion of these substrates with HO in vitro reveals that the minimal recognition site is 18 base pairs long, although several shorter substrates and substrates containing point mutations are cleaved at low levels in vitro. (pnas.org)
A 24-base-pair HO recognition site stimulates homologous recombination when present in a region unrelated to MAT. (pnas.org)

By combining name-based information from dozens of different authoritative sources like the Catalogue of Life , IRMNG and the World Register of Marine Species (affectionately known as 'WoRMS'), the backbone provides a consistent means of organizing all species-related content on GBIF.org-like datasets, occurrences and species pages-and enables all forms of taxonomic searching, browsing and reporting. (gbif.org)

A comparison between the sequencing results and bioinformatic sRNA predictions using Dynalign and RNAz revealed only a small overlap between the different approaches. (nih.gov)

the hybridization-based markers deployed in these studies have genetical and practical disadvantages, particularly in the context of applied agricultural research. (genetics.org)
Agilent offers other hybridization-based target enrichment technology options, also, for finding specific regions-of-interest. (agilent.com)
Initial strategies for exome enrichment utilized a hybridization-based capture approach. (sigmaaldrich.com)

Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. (springer.com)

Humm A, Huber R, Mann K. The amino acid sequences of human and pig L-arginine:glycine amidinotransferase. (labome.org)
Can Foldit be used to predict a tertiary structure based on the primary sequence or amino acid sequence? (fold.it)
Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start site. (wikipedia.org)
citation needed] In F1 phage, a class of viruses that infect bacteria, the sequence coding for the first few amino acids often contains termination triplets in the two unused reading frames. (wikipedia.org)

This came from their observation that the 3' terminal sequences of 18S rRNA from Drosophila melanogaster, Saccharomyces cerevisiae, and rabbit cells are identical: GAUCAUUA -3'OH. (wikipedia.org)

This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach. (sigmaaldrich.com)

To enable the application of deep learning in biology, we present Selene ( https://selene.flatironinstitute.org/ ), a PyTorch-based deep learning library for fast and easy development, training, and application of deep learning model architectures for any biological sequence data. (nature.com)
We demonstrate on DNA sequences how Selene allows researchers to easily train a published architecture on new data, develop and evaluate a new architecture, and use a trained model to answer biological questions of interest. (nature.com)
ENCODE: Encyclopedia of DNA Elements https://www.encodeproject.org/data-standards/reference-sequences/ (2016). (nature.com)
A ) Expression of eight out of twelve new candidate sRNAs could be confirmed by northern blotting whereas the length of the probed RNA corresponded to the calculated length from the sequencing data. (nih.gov)
Sequencing of fragments produces data in the form of fragment counts ( X ). Similarly, a control experiment ( Right ) measures natural drop-off (fragments labeled Y ). The model parameters consist of the adduct probabilities (Θ), the Poisson rate for the number of adducts per molecule ( c ), and the drop-off probabilities in the control experiment (Γ). (pnas.org)
INSTALLATION See installation instructions: http://code.google.com/p/sequor/wiki/INSTALL USAGE With Sequor you can learn a model from sequences manually annotated with labels, and then apply this model to new data in order to add labels. (haskell.org)
In this thesis, we focus on the base-calling stage, during which base order is estimated from data collected through electrophoresis and florescence detection. (mit.edu)
As disease detection technologies rapidly evolve, so too must the FDA's approach to reviewing these new innovations," said FDA Commissioner Scott Gottlieb, M.D. "The new policies issued today provide a modern and flexible framework to generate data needed to support the FDA's review of NGS-based tests, and give developers new tools to support the efficient development and validation of these technologies. (fda.gov)
Its main advantages are: fast and selective data access plans, and intelligent combination of such plans, based on a summary of the document paths. (sciweavers.org)
Comparison of the sequence data with that of other known actin-capping and severing proteins shows no significant homologies, suggesting that Cap Z may be a member of a unique group of capping, nonsevering proteins. (labome.org)
This Ph.D. Dissertation inferred the historical processes that seem to have built the avian community assemblage restricted to the Amazonian floodplains based on their patterns of diversification and geological and climatic data. (usp.br)
We evaluate the method on simulated and real datasets from droplet-based and full-length protocols, and show that the flexible inference framework is capable of yielding biological insights through a clear interpretation of the data. (biorxiv.org)

Using a method developed by Hunt, Shine and Dalgarno showed that the nucleotide tract at the 3' end of E. coli 16S ribosomal RNA (rRNA) (that is, the end where translation begins) is pyrimidine-rich and has the specific sequence YACCUCCUUA. (wikipedia.org)

Results show that the use of exponential decay weighting schemes when taking into account non contiguous sequences to compute recommendations enhances the accuracy. (inria.fr)

We will first identify the isolates by 16S rDNA sequencing. (criver.com)
Sequences of isolates from 52 unrelated patients were divided into 29 different sequence types, giving a discriminatory index of 0.95. (asm.org)

If you're curious to see how P ROB C ONS performs on nucleotide sequence, try out P ROB C ONS RNA , an experimental version of P ROB C ONS with parameters estimated via unsupervised training on BRAliBASE II ! (stanford.edu)

Algorithms that use such sequences may have superior convergence. (fsu.edu)

The advent of DNA sequencing has revolutionized biological research by providing virtual blueprints of living organisms and offering insights into complicated biochemical processes. (mit.edu)
Each species hypothesis is assigned a DOI , establishing a stable, permanent reference for that particular hypothesis (sequences known to derive from organisms already in possession of formally described Linnaean scientific names can, of course, rely on those). (gbif.org)
However, it is now clear that inheritance not based on DNA sequence exists in multiple organisms, with examples found in microbes, plants, and invertebrate and vertebrate animals. (sciencemag.org)
Yet, it appears that biology is much richer: Many phenomena and mechanisms of nongenetic and/or non-DNA sequence-based inheritance have been described in a range of model organisms, challenging our perception of the well-established relationship between transmitted genotype and phenotype. (sciencemag.org)
Examples of non-DNA sequence-based inheritance and/or the inheritance of acquired traits have recently been reviewed elsewhere ( 7 - 11 ) and span many diverse organisms. (sciencemag.org)

Write the base sequence for the mRNA that would be formed during transcription from the DNA strand with the base sequence GCCATATTG. (bartleby.com)
Base pairing between the 3'-end of the rRNA and the Shine-Dalgarno sequence in mRNA is a mechanism by which the cell can distinguish between initiator AUGs and internal and/or out-of-frame AUG sequences. (wikipedia.org)
This change is due to a reduced or increased mRNA-ribosome pairing efficiency, as evidenced by the fact that compensatory mutations in the 3'-terminal 16S rRNA sequence can restore translation. (wikipedia.org)

HTG Edge system capabilities have been expanded to fully automate sample and targeted library preparation for next-generation sequencing. (cnbc.com)
Cancer Research UK has launched the Genomics Initiative, a series of nine research projects that will use next-generation sequencing "to address specific research questions that until now were impossible to answer," the charity said last week. (genomeweb.com)
Richard Marais from the Institute of Cancer Research in London will analyze the genomes of rare melanoma subtypes by next-generation sequencing to discover new drivers and therapeutic targets. (genomeweb.com)
Dominique Bonnet from Cancer Research UK's London Research Institute will perform next-generation sequencing of leukemic stem cell fractions. (genomeweb.com)
CARLSBAD, Calif.--( BUSINESS WIRE )-- Thermo Fisher Scientific , the world leader in serving science, has entered into a long-term agreement with Novartis and Pfizer to develop and commercialize a multi-marker, universal next-generation sequencing (NGS) oncology test that will serve as a companion diagnostic (CDx) for non-small cell lung cancer (NSCLC) across multiple drug development programs. (businesswire.com)
Starting with low-passaged, authenticated ATCC materials and using a standardized next-generation sequencing and hybrid assembly approach, ATCC produced complete reference-quality genomes by combining highly accurate short reads with the scaffolding ability of ultra-long reads. (atcc.org)

Our new NEBNext® Ultra™ II FS DNA Library Prep Kit with novel fragmentation reagent meets the dual challenge of generating high quality next gen sequencing libraries from ever-decreasing input amounts AND simple scalability. (neb.com)
A ) Length distribution of reads after 5′ end-linker and polyA-tail clipping of four sequenced C. trachomatis cDNA libraries generated from either total RNA or total RNA enriched for primary transcripts of reticulate bodies (RB) or elementary bodies (EB), respectively. (nih.gov)
B ) Sequence read distribution of the four cDNA libraries grouped into different classes of RNAs. (nih.gov)
Here we report the discovery, characteristics, development, and linkage mapping of 568 new barley SSRs from enriched small insert libraries and from new sequences in the public databases. (genetics.org)

The Shine-Dalgarno sequence is common in bacteria, but rarer in archaea. (wikipedia.org)

In order to use sequence prediction, we need to sequentialize these logical forms. (inria.fr)

Forty had the same sequence type in consecutive specimens. (asm.org)
Specimens collected from two men were repeatedly positive at intervals of 472 and 1,395 days, respectively, but the sequence types had changed. (asm.org)
Seventy-nine M. genitalium -positive specimens from 19 couples were investigated, and all partners initially had concordant sequence types, but one couple had discordant types at one time point before a newly introduced strain took over. (asm.org)
But without physical specimens or accepted scientific names, these sequences cannot not be linked to the Linnaean-based nomenclature Codes that set the rules governing the biological classification system. (gbif.org)

The detection can be performed by direct sequencing of the cDNA fragments using high-throughput sequencing technology ( 2 ). (pnas.org)
The identification of adduct formation can be performed by capillary electrophoresis (SHAPE-CE) or by high-throughput sequencing of cDNA fragments (SHAPE-Seq) ( 2 ) ( Fig. 1 ). (pnas.org)

For building the optimized test schedule, frequency based pseudo damage methodology called Relative Damage Spectrum (RDS) is incorporated.This method enhances the proving ground durability validation process by providing optimized test schedules to prevent redundant vehicle testing. (sae.org)
The Cr-based compound structure shows excellent sensitivity and selectivity which can make it a promising methodology for DNA sequencing. (osapublishing.org)

and uses ordered sequences as logical and physical structures. (sciweavers.org)
We propose novel nano-plasmonic-based structures for rapid sequencing of DNA molecules. (osapublishing.org)

sequence A090822 in the OEIS) The sequence is similar in definition to the Kolakoski sequence, but instead of counting the longest run of single terms, the sequence counts the longest run of blocks of terms of any length. (wikipedia.org)

In hope of addressing this gap in scientific knowledge, experts from the University of Tartu Natural History Museum (home to the GBIF Estonia node) and the University of Gothenburg developed UNITE , a system that uses ribosomal DNA-based sequences to give an identity to these cryptic elements of fungal biodiversity. (gbif.org)

Our sequence-based strain typing can help you map your microbial environment. (criver.com)
SeCore® Kits are our latest line of high-resolution HLA typing products based on sequence-based typing-the 'gold standard' of allele identification. (thermofisher.com)
The aim of the present study was to document, by DNA-based typing, that M. genitalium is transmissible through sexual contact. (asm.org)

For bases b ≤ 5 and exponents e ≥ 2, there exist arbitrarily long finite sequences of d -consecutive e -power b -happy numbers for a specific d = d ( e,b ), which is shown to be minimal possible. (emis.de)
Though it is known that each natural number occurs at a finite position within the sequence, it has been conjectured that the sequence may have a finite mean. (wikipedia.org)

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. (psu.edu)
Our results can be easily extended to other chemical probes of RNA structure, and also generalized to modeling polymerase drop-off in other sequence census-based experiments. (pnas.org)

The resulting DNA sequences, or sequence types, are compared to others in a database and the relationships displayed in a phylogenetic tree. (criver.com)

Comparative phylogeography of floodplain specialist birds based on sequences of ultra. (usp.br)

Shown are relative numbers of groups of sequence length in relation to the total number of reads per library. (nih.gov)
Following sequencing, reads are mapped back to the RNA sequence and are classified by their end location. (pnas.org)

Mutations in the Shine-Dalgarno sequence can reduce or increase translation in prokaryotes. (wikipedia.org)

This paper describes a new approach of generating suitable recommendations based on the active user's navigation stream. (inria.fr)
In this new approach, the bases forming the backbone of the typical DNA molecule are viewed one by one in the act of replicating. (nanotech-now.com)
The approach has led to the definition of more than 73,000 fungal species hypotheses, which together rely on and combine more than half of the system's 817,130 public reference DNA sequences. (gbif.org)
To this end, we propose an alternative to the traditional subject domain specific design approach which is based on the use of competence description ontology and learner's competence records. (sciweavers.org)
MRI of acute myocarditis: a comprehensive approach based on various imaging sequences. (biomedsearch.com)

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)
The work has now been published in Biomaterials Science ( http://pubs.rsc.org/en/content/articlelanding/2013/bm/c3bm60126a#!divAbstract ) and presentations on the work by first author, Giovanna Sicilia, have won First Prizes at the UK and Ireland Controlled Release Society and the Macro Group UK Young Researchers' Meeting. (nottingham.ac.uk)

A family of quaternary periodic complementary sequence (PCS) or Z-complementary sequence (PZCS) sets is presented. (aimsciences.org)
further explanation needed] In a commentary on this paper, it was noted that complementary base pairing with the 3'-terminus of 16S rRNA might serve to abort peptide bond formation after out-of-phase initiation. (wikipedia.org)

Sequences that track iterators must derived from _Safe_sequence_base publicly, so that safe iterators (which inherit _Safe_iterator_base ) can attach to them. (ubuntu.com)

Agilent׷ SureMASTR technology is based on multiplex PCR and amplifies multiple genomic targets through a simple PCR experiment. (agilent.com)
Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in vertebrates. (wikipedia.org)

The original code can only compute the "next" element of the sequence. (fsu.edu)

Anatomy2

Organisms4

Diseases1

Chemicals and Drugs41

Analytical, Diagnostic and Therapeutic Techniques and Equipment16

Phenomena and Processes41

Disciplines and Occupations1

Information Science6

Health Care2

Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/178859)

Marker effects on reversion of T4rII mutants. (2/178859)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (3/178859)

Regulation of body length and male tail ray pattern formation of Caenorhabditis elegans by a member of TGF-beta family. (4/178859)

Activation of systemic acquired silencing by localised introduction of DNA. (5/178859)

Molecular cloning and epitope analysis of the peanut allergen Ara h 3. (6/178859)

TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. (7/178859)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (8/178859)

Base Sequence

Base Pairing

Nucleic Acid Conformation

DNA

Base Composition

Nucleic Acid Denaturation

Molecular Sequence Data

Nucleic Acid Renaturation

Oligonucleotides

Nucleic Acid Hybridization

Oligodeoxyribonucleotides

Polydeoxyribonucleotides

Aminacrine

DNA, Viral

DNA, Bacterial

RNA, Ribosomal, 18S

Escherichia coli

Poly dA-dT

Cloning, Molecular

RNA, Ribosomal

Skull Base

Guanine

Sequence Homology, Nucleic Acid

DNA, Circular

Amino Acid Sequence

Genes

Saccharomyces

Schiff Bases

Intercalating Agents

Plasmids

Models, Molecular

RNA

Adenine

Saccharomycetales

DNA Restriction Enzymes

Mutation

Repetitive Sequences, Nucleic Acid

RNA, Viral

Transcription, Genetic

DNA, Single-Stranded

Deoxyribonucleotides

Species Specificity

Thermodynamics

Poly A

Tritium

Coliphages

RNA, Messenger

Kinetics

Oligoribonucleotides

Hybridization, Genetic

Temperature

Chemistry

Genes, Bacterial

RNA, Bacterial

Chemical Phenomena

Nucleotides

RNA, Fungal

Binding Sites

Genes, Viral

Restriction Mapping

Hot Temperature

Transformation, Genetic

Magnetic Resonance Spectroscopy

Templates, Genetic

Molecular Weight

Centrifugation, Density Gradient

DNA, Recombinant

Ribonucleases

Endonucleases

Phylogeny

Substrate Specificity

DNA Probes

Cell Line

Structure-Activity Relationship

DNA Replication

Polymerase Chain Reaction

Skull Base Neoplasms

Promoter Regions, Genetic

DNA Primers

Models, Chemical