Consensus Sequence
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Molecular Sequence Data
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.
Base Sequence
Consensus
Amino Acid Sequence
Promoter Regions, Genetic
Binding Sites
Cloning, Molecular
Transcription, Genetic
Sequence Homology, Nucleic Acid
Sequence Alignment
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.
DNA
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).
Sequence Homology, Amino Acid
DNA-Binding Proteins
Transcription Factors
Consensus Development Conferences as Topic
Presentations of summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus--often with findings and recommendations--on a subject of interest. The Conference, consisting of participants representing the scientific and lay viewpoints, is a significant means of evaluating current medical thought and reflects the latest advances in research for the respective field being addressed.
Sequence Analysis, DNA
Plasmids
Escherichia coli
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.
Protein Binding
Restriction Mapping
Regulatory Sequences, Nucleic Acid
Mutagenesis, Site-Directed
Mutation
Introns
Repetitive Sequences, Nucleic Acid
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).
RNA, Messenger
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.
Interferon Regulatory Factors
A family of transcription factors that share an N-terminal HELIX-TURN-HELIX MOTIF and bind INTERFERON-inducible promoters to control GENE expression. IRF proteins bind specific DNA sequences such as interferon-stimulated response elements, interferon regulatory elements, and the interferon consensus sequence.
DNA Primers
Genes
Gene Expression Regulation
DNA, Complementary
Polymerase Chain Reaction
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.
Recombinant Fusion Proteins
Repressor Proteins
Conserved Sequence
Transfection
Exons
Oligodeoxyribonucleotides
RNA Splicing
Nucleic Acid Conformation
Gene Expression Regulation, Bacterial
Operon
Amino Acid Motifs
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Enhancer Elements, Genetic
Substrate Specificity
Saccharomyces cerevisiae
Gene Library
Nuclear Proteins
Genes, Regulator
Chloramphenicol O-Acetyltransferase
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Delphi Technique
Sequence Analysis
Chromosome Mapping
HeLa Cells
DNA Restriction Enzymes
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.
Models, Molecular
Response Elements
DNA Footprinting
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Oligonucleotide Probes
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Deoxyribonuclease I
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Phosphorylation
Open Reading Frames
Trans-Activators
Zinc Fingers
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Carrier Proteins
Glycosylation
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Transcriptional Activation
Genes, Reporter
Structure-Activity Relationship
RNA
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)
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Sp1 Transcription Factor
Point Mutation
Blotting, Northern
Blotting, Southern
Furin
Peptide Fragments
Mutagenesis
Genomic Library
Oligonucleotides
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
RNA Precursors
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Species Specificity
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.
Cell Nucleus
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Gene Expression
Evolution, Molecular
Peptide Library
RNA Splice Sites
Cells, Cultured
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Interferon Regulatory Factor-2
TATA Box
Nucleic Acid Hybridization
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)
Protein Biosynthesis
Gene Expression Regulation, Enzymologic
Binding, Competitive
Software
Tumor Cells, Cultured
Alternative Splicing
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Membrane Proteins
Electrophoresis, Polyacrylamide Gel
Algorithms
Cricetinae
DNA-Directed RNA Polymerases
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).
RNA-Binding Proteins
Consensus Development Conferences, NIH as Topic
Articles on conferences sponsored by NIH presenting summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus on a subject of interest. This heading is used for NIH consensus conferences as a means of scientific communication. In indexing it is viewed as a type of review article and as a tag for any article appearing in any publication of the NIH Office of Medical Applications of Research (OMAR).
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Protein Structure, Secondary
Sigma Factor
DNA Probes
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.
Expressed Sequence Tags
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
beta-Galactosidase
5' Untranslated Regions
Chickens
Saccharomyces cerevisiae Proteins
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Serine
Models, Genetic
Cattle
Regulon
Transcription Initiation Site
Interferon Regulatory Factor-1
Lorisidae
A family of Primates of the suborder Strepsirhini containing six genera. The family is distributed in parts of Africa, India, Asia, and the Philippines. The six genera are: Arctocebus (golden potto), GALAGO (bush babies), Loris (slender loris), Nycticebus (slow loris), and Perodicticus (potto). Lorises and pottos are relatively common except for Arctocebus, the golden potto. All are arboreal and nocturnal.
Organ Specificity
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
DNA, Recombinant
RNA, Small Nuclear
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
Luciferases
Reverse Transcriptase Polymerase Chain Reaction
Blotting, Western
Sequence Analysis, Protein
5' Flanking Region
Peptide Mapping
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Mutagenesis, Insertional
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
DNA, Satellite
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Heat-Shock Proteins
Contig Mapping
Replication Origin
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Genetic Complementation Test
3T3 Cells
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
Integration Host Factors
Genetic Vectors
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Proto-Oncogene Proteins
Sequence Homology
Signal Transduction
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Short Interspersed Nucleotide Elements
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
CHO Cells
Macromolecular Substances
Protein Kinases
Operator Regions, Genetic
RNA, Bacterial
Poly A
Gene Deletion
Precipitin Tests
Chromatin Immunoprecipitation
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Drosophila melanogaster
Protein Sorting Signals
Transcription Factor AP-1
Lac Operon
Proline
Phenotype
COS Cells
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Concomitant activation of pathways downstream of Grb2 and PI 3-kinase is required for MET-mediated metastasis. (1/4818)
The Met tyrosine kinase - the HGF receptor - induces cell transformation and metastasis when constitutively activated. Met signaling is mediated by phosphorylation of two carboxy-terminal tyrosines which act as docking sites for a number of SH2-containing molecules. These include Grb2 and p85 which couple the receptor, respectively, with Ras and PI 3-kinase. We previously showed that a Met mutant designed to obtain preferential coupling with Grb2 (Met2xGrb2) is permissive for motility, increases transformation, but - surprisingly - is impaired in causing invasion and metastasis. In this work we used Met mutants optimized for binding either p85 alone (Met2xPI3K) or p85 and Grb2 (MetPI3K/Grb2) to evaluate the relative importance of Ras and PI 3-kinase as downstream effectors of Met. Met2xPI3K was competent in eliciting motility, but not transformation, invasion, or metastasis. Conversely, MetP13K/Grb2 induced motility, transformation, invasion and metastasis as efficiently as wild type Met. Furthermore, the expression of constitutively active PI 3-kinase in cells transformed by the Met2xGrb2 mutant, fully rescued their ability to invade and metastasize. These data point to a central role for PI 3-kinase in Met-mediated invasiveness, and indicate that simultaneous activation of Ras and PI 3-kinase is required to unleash the Met metastatic potential. (+info)ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (2/4818)
To understand the mechanism of Ly49A-expression and its significance in T-cell differentiation, we analyzed the 5'-flanking region of the Ly49A gene in a search for the Ly49A-regulatory element. Since very few known regulatory elements have been found in this region, presumably a novel regulatory sequence(s) could exist. Accordingly, we defined the 13-bp regulatory element, 5'-ATGACGAGGAGGA-3', restricted to Ly49A-expression in EL-4 cells in comparison with two other representative cell lines tested. This element, designated as EL13, proved to be previously undiscovered by homology search and is highly homologous with several virus DNAs. Using EL13 as a probe we have cloned a cDNA encoding a binding protein to EL13. Its deduced nucleotide sequence revealed that EL13-binding protein is almost identical with rat ATF-2. Although ATF-2 is known to bind to cyclic AMP responsive element (CRE), EL13 shares five out of eight nucleotides with this consensus sequence. Our results suggested that ATF-2 may play an important role via binding to EL13 for the expression of Ly49A. These data will provide useful information for understanding T-cell and NK-cell differentiation in murine immune system. (+info)Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. (3/4818)
The expression of a luciferase reporter gene under the control of the human glucose 6-phosphatase gene promoter was stimulated by both dexamethasone and dibutyryl cAMP in H4IIE hepatoma cells. A cis-active element located between nucleotides -161 and -152 in the glucose 6-phosphatase gene promoter was identified and found to be necessary for both basal reporter-gene expression and induction of expression by both dibutyryl cAMP and dexamethasone. Nucleotides -161 to -152 were functionally replaced by the consensus sequence for a cAMP response element. An antibody against the cAMP response element-binding protein caused a supershift in gel-electrophoretic-mobility-shift assays using an oligonucleotide probe representing the glucose 6-phosphatase gene promoter from nucleotides -161 to -152. These results strongly indicate that in H4IIE cells the glucose 6-phosphatase gene-promoter sequence from -161 to -152 is a cAMP response element which is important for the regulation of transcription of the glucose 6-phosphatase gene by both cAMP and glucocorticoids. (+info)Analysis of 4-phosphopantetheinylation of polyhydroxybutyrate synthase from Ralstonia eutropha: generation of beta-alanine auxotrophic Tn5 mutants and cloning of the panD gene region. (4/4818)
The postulated posttranslational modification of the polyhydroxybutyrate (PHA) synthase from Ralstonia eutropha by 4-phosphopantetheine was investigated. Four beta-alanine auxotrophic Tn5-induced mutants of R. eutropha HF39 were isolated, and two insertions were mapped in an open reading frame with strong similarity to the panD gene from Escherichia coli, encoding L-aspartate-1-decarboxylase (EC 4.1.1.15), whereas two other insertions were mapped in an open reading frame (ORF) with strong similarity to the NAD(P)+ transhydrogenase (EC 1.6.1.1) alpha 1 subunit, encoded by the pntAA gene from Escherichia coli. The panD gene was cloned by complementation of the panD mutant of R. eutropha Q20. DNA sequencing of the panD gene region (3,312 bp) revealed an ORF of 365 bp, encoding a protein with 63 and 67% amino acid sequence similarity to PanD from E. coli and Bacillus subtilis, respectively. Subcloning of only this ORF into vectors pBBR1MCS-3 and pBluescript KS- led to complementation of the panD mutants of R. eutropha and E. coli SJ16, respectively. panD-encoded L-aspartate-1-decarboxylase was further confirmed by an enzymatic assay. Upstream of panD, an ORF with strong similarity to pntAA from E. coli, encoding NAD(P)+ transhydrogenase subunit alpha 1 was found; downstream of panD, two ORFs with strong similarity to pntAB and pntB, encoding subunits alpha 2 and beta of the NAD(P)+ transhydrogenase, respectively, were identified. Thus, a hitherto undetermined organization of pan and pnt genes was found in R. eutropha. Labeling experiments using one of the R. eutropha panD mutants and [2-14C]beta-alanine provided no evidence that R. eutropha PHA synthase is covalently modified by posttranslational attachment of 4-phosphopantetheine, nor did the E. coli panD mutant exhibit detectable labeling of functional PHA synthase from R. eutropha. (+info)An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (5/4818)
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus. (+info)Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (6/4818)
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes. (+info)A binding site for homeodomain and Pax proteins is necessary for L1 cell adhesion molecule gene expression by Pax-6 and bone morphogenetic proteins. (7/4818)
The cell adhesion molecule L1 regulates axonal guidance and fasciculation during development. We previously identified the regulatory region of the L1 gene and showed that it was sufficient for establishing the neural pattern of L1 expression in transgenic mice. In the present study, we characterize a DNA element within this region called the HPD that contains binding motifs for both homeodomain and Pax proteins and responds to signals from bone morphogenetic proteins (BMPs). An ATTA sequence within the core of the HPD was required for binding to the homeodomain protein Barx2 while a separate paired domain recognition motif was necessary for binding to Pax-6. In cellular transfection experiments, L1-luciferase reporter constructs containing the HPD were activated an average of 4-fold by Pax-6 in N2A cells and 5-fold by BMP-2 and BMP-4 in Ng108 cells. Both of these responses were eliminated on deletion of the HPD from L1 constructs. In transgenic mice, deletion of the HPD from an L1-lacZ reporter resulted in a loss of beta-galactosidase expression in the telencephalon and mesencephalon. Collectively, our experiments indicate that the HPD regulates L1 expression in neural tissues via homeodomain and Pax proteins and is likely to be a target of BMP signaling during development. (+info)Functional analysis of the promoter of the yeast SNQ2 gene encoding a multidrug resistance transporter that confers the resistance to 4-nitroquinoline N-oxide. (8/4818)
The yeast gene SNQ2, which encodes a multidrug resistance ABC superfamily protein, is required for resistance to the mutagen 4-nitroquinoline N-oxide (4-NQO). The expression of the SNQ2 gene is under the control of a regulatory network that involves the transcription factor Yrr1p, as well as Pdr1p/Pdr3p (Cui et al., Mol. Microbiol., 29, 1307-1315 (1998)). By 5'-deletion analysis of the promoter by using SNQ2-lacZ fusion constructs, four regions: -745 to -639 (region I), -639 to -578 (region II), -548 to -533 (region III) and -533 to -485 (region IV) were found to be important for SNQ2 expression. Genetic analysis suggested that the site in region IV was responsible for the Yrr1p-mediated SNQ2 expression. A consensus motif known for the binding of Pdr1p/Pdr3p (PDRE) was not found in region IV. (+info)
NIOSHTIC-2 Publications Search - 20038418 - A novel mechanism for p53 to regulate its target gene ECK in signaling apoptosis.
Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension
The Natural Complexity of Patent Eligibility - Iowa Law Review - The University of Iowa College of Law
release history
release history
Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers
blockchain - New params of chainparams.cpp. What put on them and how generate? - Bitcoin Stack Exchange
cluster # 2681
20284 (consensus weight case 2b3 does not follow dir-spec)
- Tor Bug Tracker & Wiki
How to Build Consensus in a Collaboration Team | UniversalClass
Bio-software] Software for aligning abi trace files
On the Misgivings of Anthropomorphic Consensus Polling in Defining the Complexity of Life
Wider-than-Expected Q3 Loss at Alnylam
PEDIATRIC ANIMAL MODEL OF GROWTH RETARDATION IN AIDS
- UC Davis
Kozak consensus sequence - Wikipedia
Author Search Results
Virus mystery homepage
Virus mystery homepage
OPENSEQ.org - FTSW RODA SPOVE - Pfam Coevolution Predictions
BIP 0123 - Bitcoin Wiki
CCDS Report for Consensus CDS
CCDS Report for Consensus CDS
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination - Page 3
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination - Page 2
What the critics wrote about the Beatles in 1964 - Daily Press
Secondary structure prediction and consensus sequence o | Open-i
Protein consensus sequence motifs | SpringerLink
Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close...
Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus...
Zinc finger and BTB domain-containing protein 4
P16-13. A greater breadth of HIV-1-specific T cell responses detected using mosaic peptides compare to consensus peptides -...
Hella Heaven: There is no such thing as consensus science Michael Crichton
in-vitro systems
ArchDB - Biological DataBase of Protein Loops
The Markets Assessment of the Probability of Meeting or Beating the Consensus by Guang Ma, Stanimir Markov :: SSRN
Cel-Sci Corporation - Consensus Indicates Potential 62.4% Upside
Copenhagen Consensus: Whats more important, growing more food or controlling the world population?
HP Q1 adj. EPS 92 cents vs. 65 cents a year ago; FactSet consensus 66 cents - The 2020 Bubble - The Year The World Popped
Italys Two Options: Hardball or Consensus
False consensus effect 彙整 - 體驗冒險的職涯實驗室 - Experiencing Experimental Career Lab.
Smo9 project
Interferon regulatory factor 8/interferon consensus sequence binding protein is a critical transcription factor for the...
Rabbit anti IRF8 Antibody (Cross) | Bio-Rad
Characterization of a functionally important and evolutionarily well-conserved epitope mapped to the short consensus repeats of...
Leader-Following Consensus of Linear Multiagent Systems with State Observer under Switching Topologies
BSORF Gene Entry : BG10678
254780372
Consensus Decision Making - ReadWriteThink
No Frakking Consensus: Pachauris Latest Award: Can You Say Conflict-of-Interest?
About myself - Uffe Ravnskov
Narrower-than-Expected Loss at Curis
DNA binding site
... restriction sites can be generally represented by consensus sequences. This is because they target mostly identical sequences ... This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are ... Schneider T.D. (2002). "Consensus sequence Zen". Applied Bioinformatics. 1 (3): 111-119. PMC 1852464. PMID 15130839. Bulyk M.L ... can be represented by a consensus sequence. This representation has the advantage of being compact, but at the expense of ...
Collagen, type III, alpha 1
"Report for CCDS2297.1". Consensus Coding Sequence (CDS) Database. National Center for Biotechnology Information (NCBI). "Ehlers ... June 1993). "Sequencing of cDNA from 50 unrelated patients reveals that mutations in the triple-helical domain of type III ... This (Gly-X-Y)n sequence is repeated 343 times in the type III collagen molecule. Proline or hydroxyproline is often found in ... June 2015). "Vascular Ehlers-Danlos Syndrome in siblings with biallelic COL3A1 sequence variants and marked clinical ...
Colin Dingwall
Nuclear targeting sequences-a consensus?. Trends in biochemical sciences. 1991 Jan 1;16:478-81. According to Google Scholar, ... Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences--a consensus?". Trends in Biochemical Sciences. 16 (12): ... Detailed mapping of the sequence in nucleoplasmin revealed a longer sequence motif within which two domains of basic amino ... nuclear localization sequence has emerged as the major nuclear localization sequence in cellular proteins and the sequence ...
SV40 large T antigen
Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences - a consensus?". Trends Biochem. Sci. 16 (12): 478-81. doi: ... Glu sequence, nor in the positions immediately flanking this sequence. The pRb-binding motif and negatively charged region ... The NLS sequence is PKKKRKV. SV40 large TAg, other polyomavirus large T antigens, adenovirus E1a proteins, and oncogenic human ... Figge J, Smith TF (14 July 1988). "Cell division sequence motif". Nature. 334 (6178): 109. doi:10.1038/334109a0. PMID 3290690. ...
GLIS1
It has the consensus sequence GACCACCCAC. The individual zinc finger motifs are separated from one another by the amino acid ... to interact with target DNA sequences to regulate gene transcription. The domain interacts sequence specifically with the DNA, ... The protein's termini are fairly unusual, and have no strong sequence similarity other proteins. Glis1 can be used as one of ... a change in a single nucleotide of the DNA sequence of the gene, has been implicated as a risk factor in the neurodegenerative ...
Circular chromosome
B) The consensus sequence of Ter. [3] The Ter sites specifically interact with the replication terminator protein called Tus in ... a 9-mer repeat with a highly conserved consensus sequence 5' - TTATCCACA - 3', that are recognized by the DnaA protein. DnaA ... Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52 ... The E. coli bacterial replication origin, called oriC consists of DNA sequences that are recognised by the DnaA protein, which ...
Short Oligonucleotide Analysis Package
SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which ... and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data. All programs in ... 2009). "The sequence and de novo assembly of the giant panda genome". Nature. 463 (7279): 311-317. doi:10.1038/nature08696. ... The first release of SOAP consisted only of the sequence alignment tool SOAPaligner. SOAP v2 extended and improved on SOAP v1 ...
Nucleic acid structure prediction
The quality of the alignment determines the accuracy of the consensus structure model. Consensus sequences are folded using ... Chiu D.K.; Kolodziejczak T. (1991). "Inferring consensus structure from nucleic acid sequences". Comput. Appl. Biosci. 7 (3): ... Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but ... A less widely used approach is to fold the sequences using single sequence structure prediction methods and align the resulting ...
Alternative splicing
... the consensus around this sequence varies somewhat. In humans the branch site consensus sequence is yUnAy. The branch site is ... The typical eukaryotic nuclear intron has consensus sequences defining important regions. Each intron has the sequence GU at ... The intron upstream from exon 4 has a polypyrimidine tract that doesn't match the consensus sequence well, so that U2AF ... Gao K, Masuda A, Matsuura T, Ohno K (April 2008). "Human branch point consensus sequence is yUnAy". Nucleic Acids Research. 36 ...
Protein methylation
Nevertheless, PRMTs with non-GAR consensus sequences exist. PRMTs are present in the nucleus as well as in the cytoplasm. In ... Proteins containing the consensus motif H2N-X-Pro-Lys- (where X can be Ala, Pro or Ser) after removal of the initiator ...
Initiator element
The consensus sequence of Inr in humans was inferred to be YYANWYY. The census sequence in Drosophila is TCAKTY. Studies have ... It has the consensus sequence YYANWYY in humans. Similarly to the TATA box, the Inr element facilitates the binding of ... Out of those sequences with the TATA box, 62% contained the Inr element as well. Though the Inr element is not fully understood ... This sequence encompasses where the RNA polymerase will begin transcribing. The Inr element is located about ~20 bp downstream ...
BRCA1
"Novel consensus DNA-binding sequence for BRCA1 protein complexes". Mol. Carcinog. 38 (2): 85-96. doi:10.1002/mc.10148. PMID ... When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are ... Zheng L, Pan H, Li S, Flesken-Nikitin A, Chen PL, Boyer TG, Lee WH (October 2000). "Sequence-specific transcriptional ... Classical methods for mutation detection (sequencing) are unable to reveal these types of mutation. Other methods have been ...
Tektin
They have the consensus amino acid sequence of RPNVELCRD. Different types of tektins, designated as A (53 kDa), B (51 kDa), C ( ... Amino acid sequences of tektins are well conserved, with significant similarity between mouse and human homologs. Tubulin ... The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur ...
Lipid-anchored protein
No consensus sequence for protein palmitoylation has been identified. Palmitoylated proteins are mainly found on the ... In the CAAX box sequence, the C represents the cysteine that is prenylated, the A represents any aliphatic amino acid and the X ... This reaction is facilitated by N-myristoyltransferase . These proteins usually begin with a Met-Gly sequence and with either a ...
GOLGA8H
Its sequence only partially matches a Kozak consensus sequence. The predicted secondary structure of GOLGA8H is composed of 81 ... A multiple sequence alignment (MSA) of GOLGA8H and its top seven paralogs was created using Clustal Omega [1]. [Appendix A] All ... The sequence for this site is NGS. N-linked glycosylation functions intrinsically and extrinsically to assist in regulating the ... "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-05-15. "ExPASy". web.expasy.org. ...
USF2
"Novel consensus DNA-binding sequence for BRCA1 protein complexes". Molecular Carcinogenesis. 38 (2): 85-96. doi:10.1002/mc. ... Groenen PM, Garcia E, Debeer P, Devriendt K, Fryns JP, Van de Ven WJ (Dec 1996). "Structure, sequence, and chromosome 19 ... "Large-scale concatenation cDNA sequencing". Genome Research. 7 (4): 353-8. doi:10.1101/gr.7.4.353. PMC 139146. PMID 9110174. ...
CAAT box
... and is typically accompanied by a conserved consensus sequence. It is an invariant DNA sequence at about minus 70 base pairs ... Some sequences lack the CAAT-box completely. Secondly, the surrounding nucleotides in plants do not match the consensus ... Both of these consensus sequences belong to the regulatory promoter. Full gene expression occurs when transcription activator ... In the direction of transcription of the template strand, the consensus sequence, or the calculated order of the most frequent ...
Insulin receptor
Pearson RB, Kemp BE (1991). "Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations". ...
Windtalkers
The site's consensus states: "The action sequences are expertly staged. Windtalkers, however, sinks under too many clichés and ...
SMAD (protein)
These motifs include the CAGAC and its CAGCC variant, as well as the 5-bp consensus sequence GGC(GC),(CG). Receptor- ... "The consensus coding sequences of human breast and colorectal cancers". Science. 314 (5797): 268-74. Bibcode:2006Sci...314.. ... are represented in the genome of all metazoans sequenced to date. The level of sequence conservation of the Co-Smad and of R- ... Phosphorylation of the R-Smad causes it to dissociate from SARA, exposing a nuclear import sequence, as well as promoting its ...
Victor Velculescu
"The consensus coding sequences of human breast and colorectal cancers". Science. New York, N.Y. 314 (5797): 268-74. Bibcode: ... In parallel, Velculescu was an early developer of methods for high-throughput sequencing of human cancer, which his group used ... PGDx was the first clinical laboratory to provide whole-exome sequencing for cancer patients in 2011. Grand Prize Winner of the ... His group also led the effort to sequence the first pediatric tumor genome for medulloblastoma. These studies defined the ...
E-box
The consensus sequence of the E-box is usually CANNTG; however, there exist other E-boxes of similar sequences called ... Furthermore, HES1, which can bind to a different consensus sequence (CACNAG, known as the N-box), shows suppression effect in ... Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is ... gene and regulates its expression CAGCTT sequence found within the MyoD core enhancer CACCTCGTGAC sequence in the proximal ...
ADAM10
The consensus sequence for catalytically active ADAM proteins is HEXGHNLGXXHD. Structural analysis of ADAM17, which has the ... March 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proceedings of the National ... The proposed active site of ADAM10 has been identified by sequence analysis, and is identical to enzymes in the Snake Venom ... same active site sequence as ADAM10, suggests that the three histidines in this sequence bind a Zn2+ atom, and that the ...
Thyroglobulin
Lamas L, Anderson PC, Fox JW, Dunn JT (1989). "Consensus sequences for early iodination and hormonogenesis in human ... Malthiéry Y, Lissitzky S (1985). "Sequence of the 5'-end quarter of the human-thyroglobulin messenger ribonucleic acid and of ... Malthiéry Y, Lissitzky S (1987). "Primary structure of human thyroglobulin deduced from the sequence of its 8448-base ... "A consensus report of the role of serum thyroglobulin as a monitoring method for low-risk patients with papillary thyroid ...
CTCF
... binds to the consensus sequence CCGCGNGGNGGCAG (in IUPAC notation). This sequence is defined by 11 zinc finger motifs in ... This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC ... Binding of targeting sequence elements by CTCF can block the interaction between enhancers and promoters, therefore limiting ... CTCF is thought to be a primary part of the activity of insulators, sequences that block the interaction between enhancers and ...
FAM231B
... contains a Kozak consensus sequence surrounding the start codon nucleotides. The primary promoter region for the human ... Its mRNA sequence is 1312 base pairs long, with the coding sequence in region 343 through 852, and there is only one exon. The ... FAM231B, or family with sequence similarity 231B, is a protein found in humans and is encoded by FAM231B gene. Orthologs of ... "Homo sapiens family with sequence similarity 231 member B (FAM231B), mRNA". National Center for Biotechnology Information, U.S ...
CD109
2006). "The consensus coding sequences of human breast and colorectal cancers". Science. 314 (5797): 268-74. Bibcode:2006Sci... ... 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805-11. Bibcode:2003Natur.425..805M. doi: ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
Calcium-binding protein 1
CAbP1 and CAbP2 contain a consensus sequence for N-terminal myristoylation. Transcription factor binding sites identified by ...
HIST1H1A
Absence of a consensus sequence for the p34cdc2/cyclin B kinase". J. Biol. Chem. 270 (46): 27653-60. doi:10.1074/jbc.270.46. ... Eick S, Nicolai M, Mumberg D, Doenecke D (Sep 1989). "Human H1 histones: conserved and varied sequence elements in two H1 ... Meergans T, Albig W, Doenecke D (1998). "Conserved sequence elements in human main type-H1 histone gene promoters: their role ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
SOS box
15 April 1998). "The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence". J. Bacteriol. 180 (8): 2201- ... Mazón G, Lucena JM, Campoy S, Fernández de Henestrosa AR, Candau P, Barbé J (February 2004). "LexA-binding sequences in Gram- ... SOS boxes differ in DNA sequences and binding affinity towards LexA from organism to organism. Furthermore, SOS boxes may be ...
MN1 (gene)
2007). "The MN1 oncoprotein activates transcription of the IGFBP5 promoter through a CACCC-rich consensus sequence". J. Mol. ...
Cushing's disease
The CRH test uses recombinant human or bovine-sequence CRH, which is administered via a 100μg intravenous bolus dose. The ... "Treatment of adrenocorticotropin-dependent Cushing's syndrome: a consensus statement". J Clin Endocrinol Metab. 93 (7): 2454- ...
Paleolithic
"Callaway, Ewen (22 September 2011), "First Aboriginal genome sequenced", Nature, Nature News, doi:10.1038/news.2011.551 ... societies may have made decisions by communal consensus decision making rather than by appointing permanent rulers such as ...
ZP3
The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage ... A variation in the last exon of this gene has previously served as the basis for an additional ZP3 locus; however, sequence and ...
Lenape
By 1860 the Delaware had reached consensus to leave Kansas, which was in accord with the government's Indian removal policy.[68 ... According to historian Steven Harper, what followed was a "convoluted sequence of deception, fraud, and extortion orchestrated ...
Brassicaceae
The APG III system has recently adopted this last solution, but this may change as a consensus arises on this point. Current ... Hall, J.C.; Sytsma, K.J.; Iltis, H.H. (2002). "Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data". ...
World Health Assembly
... by consensus) to be Geneva. A current list of members on the Executive Board can be derived through consultation of the WHA # ... sequenced and identified" a sample provided by Ali Mohamed Zaki.[20] Erasmus MC and Dr. Zaki strongly refuted all allegations ...
Talk:4 Vesta
If there is consensus for keeping the material, let it be decided here. Michaelbusch 02:32, 5 October 2006 (UTC) The only ... I think some sort of geometrically sequential arrangement is appropriate, as both indicate sequences. I think prose would be ...
Picornavirus
The CRE loop has a defined consensus sequence to which the initiation components bind, however; there is no consensus sequence ... J Virol 79(21):13385-13398 Wang X, Zhang J, Lu J, Yi F, Liu C, Hu Y. Sequence analysis and genomic organization of a new insect ... Govan VA, Leat N, Allsopp M, Davison S (2000) Analysis of the complete genome sequence of acute bee paralysis virus shows that ... Virology 277(2):457-463 Millán-Leiva A, Jakubowska AK, Ferré J, Herrero S (2011) Genome sequence of SeIV-1, a novel virus from ...
Chromosome 16
... the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number ... 2004). "The sequence and analysis of duplication-rich human chromosome 16". Nature. 432 (7020): 988-94. doi:10.1038/nature03187 ...
TATA box
Kozak consensus sequence. References[edit]. *^ a b c .mw-parser-output cite.citation{font-style:inherit}.mw-parser-output . ... The TATA box is a component of the eukaryotic core promoter and generally contains the consensus sequence 5'-TATA(A/T)A(A/T)-3 ... A CAAT box (also CAT box) is a region of nucleotides with the following consensus sequence: 5' GGCCAATCT 3'. The CAAT box is ... The TATA box consensus sequence is TATAWAW, where W is either A or T. ...
Histone
3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ... in which it became clear that there was no consensus on the number of kinds of histone and that no one knew how they would ... They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have ... Durrin LK, Mann RK, Kayne PS, Grunstein M (June 1991). "Yeast histone H4 N-terminal sequence is required for promoter ...
The Rescuers
The titular bluebird that appears in this sequence originally appeared in Alice in Wonderland (1951). ... The website's consensus states that "Featuring superlative animation, off-kilter characters, and affectionate voice work by Bob ... The Rescuers and from the opening song sequence "The Journey," was priced at $30. All figures were retired in March 2005, ...
The Shawshank Redemption
The consensus reads, "The Shawshank Redemption is an uplifting, deeply satisfying prison drama with sensitive direction and ... but with only a single night available to film the sequence, it was shortened to showing Andy standing triumphant in the water. ... and several scenes were cut including a longer sequence of Red adjusting to life after incarceration; Darabont said that in ...
Web Ontology Language
The OWL abstract syntax presents an ontology as a sequence of annotations, axioms and facts. Annotations carry machine and ... In 2005, at the OWL Experiences And Directions Workshop a consensus formed that recent advances in description logic would ...
Myers-Briggs Type Indicator
The dynamic sequence of functions and their attitudes can be determined in the following way: *The overall lifestyle preference ... consensus and fit, considering the needs of the people involved. Thinkers usually have trouble interacting with people who are ... The sequence of differentiation of dominant, auxiliary, and tertiary functions through life is termed type development. This is ... Jung's typology theories postulated a sequence of four cognitive functions (thinking, feeling, sensation, and intuition), each ...
Lactose intolerance
"NIH Consensus and State-Of-The-Science Statements (Consensus Development Conference, NIH. Review). 27 (2): 1-27. PMID 20186234 ... The specific DNA sequence in the MCM6 gene helps control whether the LCT gene is turned on or off.[19] At least several ... "NIH consensus development conference statement: Lactose intolerance and health" ...
Continuum (TV series)
The website's consensus reads, "Continuum blends time-tested genre ingredients to deliver a sci-fi crime drama that's solidly ... Starting with the third season, the narration was replaced by a new sequence that contains a computer-animated version of the ...
Race condition
A race condition arises in software when a computer program, to operate properly, depends on the sequence or timing of the ... This approach has been said to have achieved recent consensus (presumably compared to approaches which guarantee sequential ... Assume that two threads each increment the value of a global integer variable by 1. Ideally, the following sequence of ... or other system where the system's substantive behavior is dependent on the sequence or timing of other uncontrollable events. ...
Islamic calendar
... there is usually in no discernible order in the sequencing of either 29 or 30 day month lengths. Traditionally, the first day ... no consensus among scholars on this issue.[15] ...
World Bank
Though the Washington Consensus was conceived as a policy that would best promote development, it was criticized for ignoring ... in the wrong sequence or in weak, uncompetitive economies.[61][64] Similarly, Carmine Guerriero notices that these reforms have ... Joseph Stiglitz argued that the Washington Consensus placed too much emphasis on the growth of GDP, and not enough on the ... In the 1990s, the World Bank and the IMF forged the Washington Consensus, policies that included deregulation and ...
Malvales
Evidence from rbcL sequence data. American Journal of Botany 85, 876-887. (Available online: Abstract) ... a consensus has been emerging for a trend to expand Malvaceae to include these three families. This expanded circumscription of ...
Outline of brain mapping
The voltage swing sequences are recorded and broken down by positive and negative, and by how long after the stimulus they are ... The Budapest Reference Connectome server generates consensus braingraphs with selectable parameters; the graphs can be ... as the increase in temporal resolution of fMRI experiments routinely yields fMRI sequences containing several hundreds of ...
Spatial memory
The sequence length increases each trial until the participant is no longer able to replicate the pattern correctly. The test ... Although a general lack of consensus regarding this distinction has been noted in the literature, there is a growing amount of ... The experiment taps onto the blocks a sequence pattern which participants must then replicate. The blocks are numbered on the ... inner scribe is a rehearsal mechanism for visual information and is responsible for information concerning movement sequences. ...
Upgrade (film)
The website's critical consensus reads, "Like its augmented protagonist, Upgrade's old-fashioned innards get a high-tech boost ... and praised the film's dark humor and action sequences.[6] ...
Kallmann syndrome
"Expert consensus document: European Consensus Statement on congenital hypogonadotropic hypogonadism--pathogenesis, diagnosis ... new challenges in the era of oligogenism and next-generation sequencing". European Journal of Endocrinology. 178 (3): R55-R80. ...
Amyotrophic lateral sclerosis
There is no consensus among neurologists on the exact definition of familial ALS. The strictest definition is that a person ... From Genome-wide Association Mapping to Genome Sequencing". The Neuroscientist. 21 (6): 599-615. doi:10.1177/1073858414555404. ...
Silver Linings Playbook
In less than a month, Mandy Moore, a choreographer for So You Think You Can Dance, taught them the dance sequences. Moore ... The website's critical consensus reads, "Silver Linings Playbook walks a tricky thematic tightrope, but David O. Russell's ... A darker, more extreme version of the dance sequence was filmed and scenes with De Niro's character were shot in multiple ...
Indigenous Australians
"Sequencing Uncovers a 9,000 Mile Walkabout" (pdf). ICommunity Newsletter. April 2012.. *. Sharma, Kriti (9 August 2018). "The ... no consensus exists on its origins, process, or whether or not it was genocide. However, using the "UN definition, sufficient ... Callaway, E. (2011). "First Aboriginal genome sequenced". Nature. doi:10.1038/news.2011.551.. ... The sequence has been criticised as there has been no independent testing, and it has been suggested that the results may be ...
எயிட்சு - தமிழ் விக்கிப்பீடியா
1986). "Transactivation of the human immunodeficiency virus long terminal repeat sequences by DNA viruses". Proc. Natl. Acad. ... WHO HIV and Infant Feeding Technical Consultation (2006). "Consensus statement" (PDF). பார்த்த நாள் 2008-03-12. ... evidence of macaque nuclear sequences confirms substrate identity". Vaccine 23: 1639-1648. doi:10.1016/j.vaccine.2004.10.038. ...
Protein consensus sequence motifs | SpringerLink
The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include ... and consensus sequences that may be carried out on the internet.. Index Entries. Protein consensus sequences motifs protein- ... The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include ... Aitken, A. (1995) Protein chemistry methods, posttranslational modification, consensus sequences, in Proteins Labfax (Price, N ...
CiteSeerX - Sequence Logos: A New Way to Display Consensus Sequences
Sequence logos concentrate the following information into a single graphic [2]: 1. The general consensus of the sequences. ... 4. The amount of information present at every position in the sequence, measured in bits. 5. An initiation point, cut point, or ... we use logos to display aligned sets of sequences. ... RNA or protein sequences can be represented using this ... sequence logo display consensus sequence new way aligned set general consensus development center separate element following ...
GTP-binding domain: three consensus sequence elements with distinct spacing | PNAS
... including a consensus sequence composed of three consensus elements GXXXXGK, DXXG, and NKXD with consensus spacings of either ... GTP-binding domain: three consensus sequence elements with distinct spacing. T E Dever, M J Glynias, and W C Merrick ... GTP-binding domain: three consensus sequence elements with distinct spacing Message Subject (Your Name) has sent you a message ... the sequence NKXW in place of NKXD in the sequence element responsible for base specificity allows the use of ITP as well as ...
Consensus sequence - Wikipedia
... can also be considered as consensus sequences. Thus a consensus sequence is a model for a putative DNA binding site: it is ... The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are ... Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as ... A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several ...
Kozak consensus sequence - Wikipedia
The Kozak consensus sequence is so common that the similarity of the sequence around the AUG codon to the Kozak Sequence is ... The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein ... Kozak discovered the sequence through a detailed analysis of DNA genomic sequences. The Kozak sequence is not to be confused ... Kozak sequence, and leaderless initiation. Haloarchaea are known to have a variant of the Kozak consensus sequence in their ...
Consensus sequence - Biology-Online Dictionary
Consensus sequence Of a series of related dna, rna or protein sequences, the sequence that reflects the most common choice of ... The generation of consensus sequences has been subjected to intensive mathematical analysis. ... Retrieved from "https://www.biology-online.org/dictionary/index.php?title=Consensus_sequence&oldid=10105" ...
Re-evaluation of amino acid sequence and structural consensus rules for cysteine-nitric oxide reactivity. - PubMed - NCBI
Re-evaluation of amino acid sequence and structural consensus rules for cysteine-nitric oxide reactivity.. Ascenzi P1, ... or tetra-peptide consensus motif has been recognised as the Cys(Asp/Glu) pair [Stamler et al., Neuron (1997) 18, 691-696]. Here ... has been proposed as the minimum consensus motif for Cys-NO reactivity. Although not found in human Hb, the presence of a polar ... 2 position has been observed in some NO-reactive protein sequences (e.g., NMDA receptors). However, the most important ...
RCSB PDB - 1MJM: METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... sequence. Naturally occurring operators differ from the consensus sequence to a greater extent as the number of metboxes ... METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE. *DOI: 10.2210/pdb1MJM/pdb ... MetJ, while accommodating this sequence variation in natural operators, is very sensitive to particular base changes, even ...
The Consensus Coding Sequences of Human Breast and Colorectal Cancers | Science
The Consensus Coding Sequences of Human Breast and Colorectal Cancers. By Tobias Sjöblom, Siân Jones, Laura D. Wood, D. ... The Consensus Coding Sequences of Human Breast and Colorectal Cancers. By Tobias Sjöblom, Siân Jones, Laura D. Wood, D. ... The Consensus Coding Sequences of Human Breast and Colorectal Cancers Message Subject. (Your Name) has forwarded a page to you ... Sequence analysis of ,13,000 genes in breast and colorectal tumors shows that almost 200, a surprisingly large number, can be ...
The Need for a Consensus Next-generation Sequencing Panel fo... : HemaSphere
Home , Current Issue , The Need for a Consensus Next-generation Sequencing Panel fo... ... The Need for a Consensus Next-generation Sequencing Panel for Mature Lymphoid Malignancies. Sujobert, Pierre1,2; Le Bris, ... The Need for a Consensus Next-generation Sequencing Panel for Mature Lymphoid Malignancies ... For example, sequencing errors can be due to cytosine deamination during formol fixation and paraffin embedding.14,15 It is ...
Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii
This communication describes the consensus multi-locus typing scheme established by the Cryptococcal Working Group I ( ... Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii Med Mycol. 2009;47(6):561-70. ... This communication describes the consensus multi-locus typing scheme established by the Cryptococcal Working Group I ( ... Allele and sequence type information are accessible at http://www.mlst.net/ . ...
Development of the first consensus genetic map of intermediate wheatgrass ( Thinopyrum intermedium) using genotyping-by...
Key message Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools ... The_International_Barley_Genome_Sequencing_Consortium (2012) A physical, genetic and functional sequence assembly of the barley ... Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92-102CrossRefGoogle Scholar ... Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and ...
A new definition for the consensus sequence of the peroxisome targeting signal type 2
The currently accepted consensus sequence for this amino-terminal nonapeptide is -(R/K)(L/V/I)X(5)(H/Q)(L/A)-. Some C. … ... A new definition for the consensus sequence of the peroxisome targeting signal type 2 J Mol Biol. 2004 Jul 30;341(1):119-34. ... These redefined PTS2 consensus sequences will facilitate the identification of proteins of unknown cellular localization as ... The currently accepted consensus sequence for this amino-terminal nonapeptide is -(R/K)(L/V/I)X(5)(H/Q)(L/A)-. Some C.elegans ...
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. - PubMed - NCBI
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.. Gadagkar SR1, ... In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In ... We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very ... Both randomly selected and worst-case replicates were utilized to compare the consensus and concatenation approaches primarily ...
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus...
Mismatches in sequence variants are more disruptive in some duplexes than in others. Additionally, the propensity for self- ... of oligonucleotide hybridization targets common to families of aligned sequences is suggested and applied to aligned sequence ... Computer programs for the generation of multiple sequence alignments such as Clustal W allow detection of regions that are ... most conserved among many sequence variants. However, even for regions that are equally conserved, their potential utility as ...
Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus...
Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus ... Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus ... Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus ... Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus ...
IFN-γ Up-Regulates IL-18 Gene Expression Via IFN Consensus Sequence-Binding Protein and Activator Protein-1 Elements in...
IFN consensus sequence-binding protein (ICSBP)3 and AP-1 are critical elements for the maximal induction of IL-18 promoter ... Roles of IFN consensus sequence binding protein and PU.1 in regulating IL-18 gene expression. J. Immunol. 163: 2000. ... Regulation of IFN consensus sequence binding protein expression in murine macrophages. J. Immunol. 162: 7417. ... Human interferon consensus sequence binding protein is a negative regulator of enhancer elements common to interferon-inducible ...
Consensus sequence | Article about consensus sequence by The Free Dictionary
An average nucleotide sequence; each nucleotide is the most frequent at its position in the sequence Explanation of consensus ... Looking for consensus sequence? Find out information about consensus sequence. ... consensus sequence. Also found in: Dictionary, Thesaurus, Medical, Legal, Wikipedia. consensus sequence. [kən′sen·səs ‚sē·kwəns ... Then comparisons were made between the consensus sequence and the entries in the MicroSeq database.. DNA sequencing by Microseq ...
Unity in function in the absence of consensus in sequence: role of leader peptides in export | Science
How selectivity is imposed on the system in the absence of a consensus among the sequences of leader peptides is the main issue ... Unity in function in the absence of consensus in sequence: role of leader peptides in export ... Unity in function in the absence of consensus in sequence: role of leader peptides in export ... Unity in function in the absence of consensus in sequence: role of leader peptides in export ...
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. | ROSTLAB.ORG
Amino Acid Sequence, Amino Acid Substitution, Base Sequence, Consensus Sequence, Sequence Alignment, Sequence Analysis, Protein ... Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Title. Consensus sequences improve PSI- ... sequence relatedness through profile-profile comparisons are much slower and more complex than sequence-sequence and sequence- ... can be represented by consensus sequences that list the nucleic/amino acid most frequent at each sequence position in that ...
Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus...
Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ...
A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...
1 Graphical representations of G-rich sequences consensus in the HCV genome.. (A and B) A total of 1056 partial cds of the C ... Sequences of oligomers used in our studies.. * Table S5. Calculated Tm of synthetic HCV G-rich sequences in the presence of ... Sequence of the C gene for HCV JFH1 virus.. * Fig. S31. Premade sequence alignment in the central part of the HCV C gene ( ... Sequence of the C gene for HCV JFH1 virus.. Fig. S31. Premade sequence alignment in the central part of the HCV C gene (subtype ...
A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...
A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ...
Consensus document on the implementation of next generation sequencing in the genetic diagnosis of hereditary cancer | Medicina...
Consensus document on the implementation of next generation sequencing in the genetic diagnosis of hereditary cancer ... Inicio Medicina Clínica (English Edition) Consensus document on the implementation of next generation sequencing in the ge... ... Next Generation Sequencing (NGS) offers an important improvement in the efficiency of genetic diagnosis, allowing an increase ... Table 1. Minimum content of a results report from a next generation sequencing (NGS) panel of genes. It is recommended to ...
FOXM1 binds directly to non-consensus sequences in the human genome | Genome Biology | Full Text
... assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell ... FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences. ... As expected the FOXM1B DBD associates with a positive control FKH consensus sequence in a dose dependent manner (K d of 224 ± ... The first (1) shows FOXM1 binding to FKH consensus sequences in concert with recruitment of the MuvB complex present at cell ...
Simple sequence repeat-based consensus linkage map of Bombyx mori. - Semantic Scholar
... a second generation consensus silkworm genetic map with a range of 7-40 markers per linkage group and a total map length of ... cDNA sequences, and cloned random amplified polymorphic DNAs. By integrating a visible mutation p (plain, larval marking) and ... of silkworm aided by visible mutations and cleaved amplified polymorphic sequence markers developed from previously mapped ... We established a genetic linkage map employing 518 simple sequence repeat (SSR, or microsatellite) markers for Bombyx mori ( ...
Sequences similar to the consensus Ste12p binding sit | Open-i
Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 genes. ... Underlined sequences represent exact matches to the PRE consensus sequence. Mentions: An upstream regulatory element termed the ... Figure 2: Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 ... Figure 2: Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 ...
Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close...
"Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close ... Determination of the whole-genome consensus sequence of the prototype DS-1 rotavirus using sequence-independent genome ... Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed... Mlera, Luwanika; ONeill, ... Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close ...
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in...
In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the Origin ... To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and ... These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set ... exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences ...
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities | Genome Biology...
Currently, the most common targets for enrichment are the protein coding exons represented by the consensus coding DNA sequence ... We examine capture sequence data from outside of the CCDS regions and find that extremes of GC content that are present in ... This effect is due to biases inherent in both the Illumina and SOLiD sequencing platforms that are exacerbated by the capture ... We show that regions outside of the CCDS perform less efficiently in capture sequence experiments. Further, we show that the ...
ProteinsMotifsGenesAlignmentsMotifAlignmentMoleculeGenomesInterferon ConsensPromoterNucleic acid sequenceProtein sequencesEukaryoticPolymerase chain reBaylor CollegeGenotypeAmplificationCanonicalNucleotidesMultiple sequencesTarget sequencesGenomic sequencesSamtools mpileupWhole genomePeptidesHuman genomeNucleotide or amino acid seqHigh-fidelityDistantly relatedDetectionEscherichiaHighly conservedEvolutionaryHepatitis C virPacBioSpeciesVariantMolecularLociBcftools consensusMutationAnalysisGene promotersMutationalTumorHomologousOligonucleotideRegulatory sequencesMutationsGenome-wideBioinformaticsAmino acidsFastaGenerateTransposonCircular consensusPrimers
Proteins21
- Of particular note is the increasing realization of the importance for cellular regulation of protein-protein interaction motifs and sequences that target proteins to particular subcellular locations. (springer.com)
- Nuclear targeting sequences are essential for the transport of proteins into the nucleus. (nih.gov)
- Employing these features we have screened the protein sequence data base of the Protein Identification Resource and have identified only known GTP-binding proteins with the exception of protein 2C from foot-and-mouth disease virus as matching the consensus sequence. (pnas.org)
- Here, we analyse the three-dimensional structure of several proteins containing NO-reactive Cys residues, and show that their nitrosylation and denitrosylation processes may depend on the Cys-Sy atomic structural microenvironment rather than on the tri- or tetra-peptide sequence consensus motif. (nih.gov)
- The currently accepted consensus sequence for this amino-terminal nonapeptide is -(R/K)(L/V/I)X(5)(H/Q)(L/A)-. Some C.elegans proteins contain putative PTS2 motifs, including the ortholog (CeMeK) of human mevalonate kinase, an enzyme known to be targeted by PTS2 to mammalian peroxisomes. (nih.gov)
- The putative PTS2s of the proteins encoded by D1053.2 and W10G11.11 did not function in targeting to peroxisomes in yeast or mammalian cells, suggesting that the current PTS2 consensus sequence is too broad. (nih.gov)
- These redefined PTS2 consensus sequences will facilitate the identification of proteins of unknown cellular localization as possible peroxisomal proteins. (nih.gov)
- Passage of proteins across membranes during export from their site of synthesis to their final destination is mediated by leader peptides that paradoxically exhibit a unity of function in spite of a diversity of sequence. (sciencemag.org)
- Families of related genes and gene products (proteins) can be represented by consensus sequences that list the nucleic/amino acid most frequent at each sequence position in that family. (rostlab.org)
- GENTAUR suppliers human normal cells, cell lines, RNA extracts and lots of antibodies and ELISA kits to Human proteins as well as Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody. (antibody-antibodies.com)
- We systematically screened publicly available, genome scale sequence databanks and trace archives using BLAST algorithms and sequence probes derived from the enzymatic and structural proteins of representative lentiviruses. (pnas.org)
- 2006). Despite a low level of sequence similarity between PelD and PleD, we sought to determine whether there are any secondary structural similarities between these two proteins. (nih.gov)
- Multiple sequence alignments can be helpful in many circumstances like detecting historical and familial relations between sequences of proteins or amino acids and determining certain structures or locations on sequences. (wikipedia.org)
- RIN [Ripening Inhibitor] binds to DNA sequences known as the CA/T-rich-G (CArG) box, which is the general target of MADS box proteins (Ito et al. (wikidoc.org)
- Provided herein is a nucleic acid comprising consensus amino acid sequence of foot-and-mouth disease FMDV VP1-4 coat proteins of FMDV subtypes A, Asia 1, C, O, SAT1, SAT2, and SAT3 as well as plasmids and vaccines expressing the sequences. (patentsencyclopedia.com)
- A sequence alignment, produced by ClustalO , of mammalian histone proteins. (wikipedia.org)
- Sequences are the amino acids for residues 120-180 of the proteins. (wikipedia.org)
- In sequence alignments of proteins, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages. (wikipedia.org)
- Other crucial sequences of bacterial origin include DNA unwinding element (DUE, which designates the site at which oriC melts under the influence of DnaA) and binding sites for additional proteins that positively or negatively regulate the initiation process. (frontiersin.org)
- We discuss diversity of bacterial oriC regions with the main focus on roles of individual DNA recognition sequences at oriC in binding the initiator and regulatory proteins as well as the overall impact of these proteins on the formation of initiation complex. (frontiersin.org)
- Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
Motifs15
- It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. (wikipedia.org)
- Specific sequence motifs can function as regulatory sequences controlling biosynthesis, or as signal sequences that direct a molecule to a specific site within the cell or regulate its maturation. (wikipedia.org)
- The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are variable. (wikipedia.org)
- To understand these processes, we need to know which motifs are present in a sequence and which factors bind to them. (psu.edu)
- We describe a method to screen a set of DNA sequences against a precompiled library of motifs, and assess which, if any, of the motifs are statistically over- or under-represented in the sequences. (psu.edu)
- Over-represented motifs are good candidates for playing a functional role in the sequences, while under-representation hints that if the motif were present, it would have a harmful dysregulatory effect. (psu.edu)
- In each case Clover successfully detects motifs known to function in the sequences, and intriguing and testable hypotheses are made concerning additional motifs. (psu.edu)
- The nucleotide sequence patterns, or motifs, preferentially bound by various transcription factors have been collected in databases. (psu.edu)
- Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. (psu.edu)
- In mammalian DNA, this analysis reveals "consensus motifs" corresponding to functional (or putative) cis-acting elements mediating the regulation of gene expression. (edu.au)
- OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. (bioportfolio.com)
- Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences. (bioportfolio.com)
- The transcription factor AtMYB2 binds to two sequence motifs in the promoter of the Arabidopsis ADH1 gene. (genetics.org)
- Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
- Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)
Genes14
- The methionine repressor, MetJ, represses the transcription of genes involved in methionine biosynthesis by binding to arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. (rcsb.org)
- To begin a systematic analysis of such alterations, we determined the sequence of well-annotated human protein-coding genes in two common tumor types. (sciencemag.org)
- The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. (springer.com)
- The absence of congruence between the phylogenetic trees inferred from the 16S rRNA gene and the hsp65 and rpoB genes could be related to a short consensus sequence (369 bp) in a position that is not optimal for mycobacteria discrimination. (thefreedictionary.com)
- Minimum content of a results report from a next generation sequencing (NGS) panel of genes. (elsevier.es)
- Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 genes. (nih.gov)
- We searched the regions immediately upstream of the four novel FIG genes characterized in this study and found sequences matching the PRE consensus (Fig. 2). (nih.gov)
- Since several of these genes are pheromone dependent for their expression yet contain only PRE sites that differ from the consensus, these results indicate that variant PRE sites are likely to be important for Ste12p-dependent regulation of some genes (e.g. (nih.gov)
- 1992), failed to identify sequences in the upstream regions of the FIG1-4 genes closely matching the consensus binding site. (nih.gov)
- CREB (cAMP response element-binding protein) [1] is a cellular transcription factor that binds to certain DNA sequences called cAMP response elements (CRE), thereby increasing or decreasing the transcription of the genes. (wikiversity.org)
- Serum response factor (SRF) controls [smooth muscle cell] SMC gene transcription via binding to CArG box DNA sequences found within genes that exhibit SMC-restricted expression. (wikidoc.org)
- CAAT box (also CAT box) A conserved sequence found within the promoter region of the protein-encoding genes of many eukaryotic organisms. (fao.org)
- Sequence analysis of the region demonstrates a GT dinucleotide repeat, an element that resembles the neural restrictive silencer element (NRSE), which restricts transcription of neuronal genes in non-neuronal cells, and consensus sites for three families of transcription factors, Ptx1/3, Nurr1 and Gli1/2, which are required for the early differentiation of mesencephalic neurons. (duke.edu)
- Although OrgConv has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences. (biomedcentral.com)
Alignments13
- Background: Computer programs for the generation of multiple sequence alignments such as 'Clustal W' allow detection of regions that are most conserved among many sequence variants. (sciweavers.org)
- Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. (rostlab.org)
- Sequence alignments may be the most fundamental computational resource for molecular biology. (rostlab.org)
- It first predicts the CDSs supported by consensus alignments. (semanticscholar.org)
- GenomeCons is a web server to manipulate multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses. (mybiosoftware.com)
- GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences. (mybiosoftware.com)
- Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. (wikipedia.org)
- Therefore it make sense to construct an algorithm to assist in repetitive calculations of multiple sequence alignments. (wikipedia.org)
- A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (wikipedia.org)
- Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. (wikipedia.org)
- Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). (wikipedia.org)
- By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. (wikipedia.org)
- The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. (biomedcentral.com)
Motif11
- We suggest in this review that, despite this diversity, a consensus bipartite motif can be identified. (nih.gov)
- Position-specific scoring matrix Regular expression - denoting multiple sequences of symbols in formal language theory Sequence motif Sequence logo Pierce, Benjamin A. 2002. (wikipedia.org)
- The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. (wikipedia.org)
- While the +4 and the −3 positions in the Kozak sequence have the greatest relative importance in the establishing a favorable initiation context a CC or AA motif at −2 and −1 were found to be important in the initiation of translation in tobacco and maize plants. (wikipedia.org)
- Based on the human haemoglobin (Hb) structure and accounting for the known acid-base catalysed Cys beta93-nitrosylation and Cys beta393NO-denitrosylation processes, the putative amino acid sequence (Lys/Arg/His/Asp/Glu)Cys(Asp/Glu) (sites -1, 0, and + 1, respectively) has been proposed as the minimum consensus motif for Cys-NO reactivity. (nih.gov)
- However, the most important component of the tri- or tetra-peptide consensus motif has been recognised as the Cys(Asp/Glu) pair [Stamler et al. (nih.gov)
- The N-terminal regions of both subunits AddA and AddB of the Bacillus subtilis AddAB enzyme contain amino acid sequences, designated motif I, which are commonly found in ATP-binding enzymes. (asm.org)
- For both MCF7 and MDA-MB-231 cells, while only 35 and 15 % of peaks respectively contained the FKH consensus motif these were significantly enriched over background. (biomedcentral.com)
- Clover compares favorably with an ab initio motif discovery algorithm based on sequence alignment, when the motif library includes only a homolog of the factor that actually regulates the sequences. (psu.edu)
- In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
- Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
Alignment19
- In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. (wikipedia.org)
- Hello all, I want to create a consensus sequence from a Bam file I obtained through alignment. (biostars.org)
- Hi, I want to generate a consensus sequence using a bam alignment from a specific genome locati. (biostars.org)
- B. Consensus sequence of PelD and PleD was based on Phyre alignment of 20 and 100 homologues respectively. (nih.gov)
- First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. (wikipedia.org)
- A multiple sequence alignment ( MSA ) is a sequence alignment of three or more biological sequences , generally protein , DNA , or RNA . (wikipedia.org)
- Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations ( indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. (wikipedia.org)
- Multiple sequence alignment is often used to assess sequence conservation of protein domains , tertiary and secondary structures, and even individual amino acids or nucleotides. (wikipedia.org)
- Multiple sequence alignment also refers to the process of aligning such a sequence set. (wikipedia.org)
- Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. (wikipedia.org)
- When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. (wikipedia.org)
- In bioinformatics , a sequence alignment is a way of arranging the sequences of DNA , RNA , or protein to identify regions of similarity that may be a consequence of functional, structural , or evolutionary relationships between the sequences. (wikipedia.org)
- If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. (wikipedia.org)
- However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. (wikipedia.org)
- Calculating a global alignment is a form of global optimization that "forces" the alignment to span the entire length of all query sequences. (wikipedia.org)
- [4] A variety of computational algorithms have been applied to the sequence alignment problem. (wikipedia.org)
- In almost all sequence alignment representations, sequences are written in rows arranged so that aligned residues appear in successive columns. (wikipedia.org)
- Using local alignment against the published pUC18 cloning vector sequence, the position and number of errors in the consensus were identified and stored in MySQL databases. (bvsalud.org)
- The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. (biomedcentral.com)
Molecule15
- We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). (bcm.edu)
- Researchers from the University of Washington School of Medicine present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. (rna-seqblog.com)
- Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. (rna-seqblog.com)
- Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint. (elifesciences.org)
- 1. A purified and isolated nucleic acid molecule which encodes human hepatitis C virus, wherein expression of said molecule in transfected cells results in production of virus when transfected into cells, wherein said molecule encodes the amino acid sequence of SEQ ID NO:3 shown in FIGS. 14G-14H. (google.com)
- 2. The nucleic acid molecule of claim 1, wherein said molecule comprises the nucleic acid sequence of SEQ ID NO:4 shown in FIGS. 14A-14F. (google.com)
- 3. A cassette vector for cloning viral genomes, comprising, inserted therein, the nucleic acid sequence according to claim 1, said vector reading in the correct phase for the expression of said inserted molecule and having an active promoter molecule upstream thereof. (google.com)
- 7. A purified and isolated nucleic acid molecule acid molecule which encodes human hepatitis C virus, wherein expression of said molecule in transfected cells results in production of virus, wherein said molecule encodes the amino acid sequence of SEQ ID NO: 1 shown in FIGS. 4G-4H. (google.com)
- 10. The nucleic acid molecule of claim 9, wherein said molecule encodes the amino acid sequence of SEQ ID NO:5 shown in FIGS. 16G-16H. (google.com)
- 11. The nucleic acid molecule of claim 10, wherein said molecule comprises the nucleic acid sequence of SEQ ID NO:6 shown in FIGS. 16A-16F. (google.com)
- The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. (google.com)
- In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. (google.com)
- Here we investigate the utility of Pacific Biosciences single molecule real-time SMRT circular consensus sequencing CCS as an alternative to traditional cloning and Sanger sequencing PCR amplicons for gene family characterization. (duhnnae.com)
- In order to produce a high- quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. (bvsalud.org)
- Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are frequently thought to be a good way to generate reliable sequences. (bvsalud.org)
Genomes4
- We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species' allohexaploid nature (2 n = 6 x = 42) and homology to Triticeae genomes. (springer.com)
- Through mapping the sequence tags to the diploid (2 n = 2 x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. (springer.com)
- In British patent application no. 8525252 (publication no. 2166445) there are described various DNA sequences which may be used as probes to hybridize individually at a number of polymorphic sites within the human and animal genomes enabling the production of a "fingerprint" composed of marked bands of differing molecular weights. (google.com.au)
- KAT and KDAC orthologs were identified in sequenced genomes ranging from glaucophytes and algae to land plants and then analyzed for evolutionary relationships. (biomedcentral.com)
Interferon Consens5
- Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody antibody storage GENTAUR recommends for long therm storage to freeze at -24 C. For short time storage up to 30 days we suggest fridge storage at 1 to 10 C. Prevent multiple freeze taw cycles of Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody. (antibody-antibodies.com)
- Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody storing antibdies for longer storage periods of the Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody we recommend - 21C or lower and for short periods lees than 1 month we suggest +5C fridge temperatures. (antibody-antibodies.com)
- Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody rabbit polyclonal These antibodies are very stable and can be stored up to 2 months at fridge temperature under 10C. (antibody-antibodies.com)
- Do not freeze taw, rather use Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody from the fridge if your use is less than 1 or 2 weeks. (antibody-antibodies.com)
- Interferon regulatory factor 8 (IRF8, also known as interferon consensus sequence binding protein) plays essential roles in development and function of the bone marrow-derived myeloid lineage. (elsevier.com)
Promoter6
- Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an up mutation. (wikipedia.org)
- These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence. (wikipedia.org)
- Each species' promoter contains a cAMP/response element (CRE) 1 consensus sequence ( [7] ) upstream of a TATA box. (wikiversity.org)
- The diagram shows an overview of the four core promoter elements B recognition element (BRE), TATA box , initiator element (Inr), and downstream promoter element (DPE), with their respective consensus sequences and their distance from the transcription start site . (wikiversity.org)
- Lastly, promoter element enrichment analyses across species revealed conserved cis-regulatory sequences that support KAT and KDAC involvement in the regulation of plant development, cold/drought stress response, as well as cellular processes such as the circadian clock. (biomedcentral.com)
- GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding . (genecards.org)
Nucleic acid sequence1
- A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. (google.com)
Protein sequences3
- Any aligned set of DNA, RNA or protein sequences can be represented using this technique. (psu.edu)
- Of a series of related dna , rna or protein sequences , the sequence that reflects the most common choice of base or amino acid at each position . (biology-online.org)
- Although not found in human Hb, the presence of a polar amino acid residue (Gly/Ser/Thr/Cys/Tyr/Asn/Gln) at the -2 position has been observed in some NO-reactive protein sequences (e.g. (nih.gov)
Eukaryotic1
- 500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with incomplete assemblies, which explains why considerable effort and resources are often spent to improve their quality after publication. (plos.org)
Polymerase chain re1
- Analysis with several oligonucleotides and restriction enzymes, which identify the mutations most common in the Mediterranean area, allowed the identification of only one mutation, namely T----C at position 6 of the first intervening sequence (IVS-I). In order to characterize the other mutation the beta gene was amplified with polymerase chain reaction and sequenced. (biomedsearch.com)
Baylor College1
- This sequence was derived from sequence data generated by Human Genome Sequencing Center at Baylor College of Medicine: the acorn worm genome. (girinst.org)
Genotype5
- The genotype (N2) and sequence of genome segment 8 of RVA/Simian-tc/ZAF/SA11-N2/1958/G3P(2) were identical to that of the bovine rotavirus O agent. (deepdyve.com)
- Hi microfuge, I am getting the same error and I mapping reads from several genotypes to one heterozygous reference and was hoping to get the consensus files for each genotype. (biostars.org)
- Does this error mean it is not possible to get the consensus for each genotype individually? (biostars.org)
- A multicenter study of NS5b hepatitis C virus (HCV) genotype determination involving 12 laboratories demonstrates that any laboratory with expertise in sequencing techniques would be able to provide a reliable HCV genotype for clinical and epidemiological purposes as long as they are provided a consensus reference sequence database. (mysciencework.com)
- The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)
Amplification4
- Dijk, Alberdina 2013-05-01 00:00:00 Whole-genome, sequence-independent amplification and 454 ® pyrosequencing of a rotavirus SA11 cell culture sample with an unknown passage history yielded consensus sequences of twelve complete genome segments. (deepdyve.com)
- iii ) Amplification and sequencing amplify the existing errors and introduce new errors (purple), further obscuring the true epimutation. (rna-seqblog.com)
- iv ) After sequencing, cDNA tags are bioinformatically matched and a consensus sequence is generated for each cDNA copy, eliminating many amplification and sequencing artifacts. (rna-seqblog.com)
- Sequence-specific, single primer amplification and detection of PCR products for identification of hepatitis viruses. (cdc.gov)
Canonical1
- These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences. (biomedcentral.com)
Nucleotides5
- A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations. (wikipedia.org)
- On the contrary, mutations that destroy conserved nucleotides in the consensus sequence are known as down mutations. (wikipedia.org)
- The sequence was defined as 5'-(gcc)gccRccAUGG-3(IUPAC nucleobase notation summarized here) where: The underlined nucleotides indicate the translation start codon, coding for Methionine. (wikipedia.org)
- For a 'strong' consensus, the nucleotides at positions +4 (i.e. (wikipedia.org)
- A "repeating sequence of nucleotides that forms a transcription or a regulatory signal" [1] is a box . (wikidoc.org)
Multiple sequences1
- In some PCR reactions multiple sequences have identical nucleotide sequences, for example if five PCR products have identical sequences a 5 will be found in this column. (cdc.gov)
Target sequences2
- Transposons act in much the same manner in their identification of target sequences for transposition. (wikipedia.org)
- Our findings suggest potential cellular RNA target sequences for WT1 and provide tools for studying the structural and functional properties of this tumour suppressor protein. (mendeley.com)
Genomic sequences2
- Kozak discovered the sequence through a detailed analysis of DNA genomic sequences. (wikipedia.org)
- Evolutionary analyses of the genomic sequences of modern-day lentiviruses have suggested a relatively recent date for their emergence, but the failure to identify any endogenous, vertically transmitted examples has meant that their longer term evolutionary history and origin remain unknown. (pnas.org)
Samtools mpileup1
- samtools mpileup: bam file to consensus sequence generation error? (biostars.org)
Whole genome5
- Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed. (deepdyve.com)
- Interestingly, for two subregion types, microRNA and predicted exons, the capture process yields higher than expected coverage when compared to whole genome sequencing. (biomedcentral.com)
- This process identified numerous, highly significant matches within the whole genome shotgun assembled sequence of the European rabbit ( Oryctolagus cuniculus ). (pnas.org)
- Because the whole genome shotgun rabbit sequences we recovered were typically 2-10 kb in length (thus rarely containing a complete viral sequence), some of these matches probably represent different parts of the same proviral insertion. (pnas.org)
- This webinar will provide a comparison of several next-generation sequencing (NGS) approaches - including short-read 16S, whole-genome sequencing (WGS), and synthetic long-read sequencing technology - for use in microbiome research studies. (genomeweb.com)
Peptides2
- How selectivity is imposed on the system in the absence of a consensus among the sequences of leader peptides is the main issue discussed here. (sciencemag.org)
- Used when sequencing peptides. (fao.org)
Human genome2
- The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail. (sciencemag.org)
- Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. (bcm.edu)
Nucleotide or amino acid seq1
- A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. (bioportfolio.com)
High-fidelity2
- High-fidelity (blue), damaged (green), and mutated (purple) RNAs were generated by in vitro transcription by T7 RNA polymerase and sequenced via ARC-seq. (rna-seqblog.com)
- However, a relevant question on this issue is how many times the sample needs to be re-sequenced to minimize costs and achieve a high-fidelity sequence? (bvsalud.org)
Distantly related1
- Relatively recent dates for the emergence of the modern lentiviral subgroups have been suggested, but these estimates are based on extrapolations of genetic distances observed among contemporary viruses, which are likely to be unreliable for evolutionary comparison of distantly related sequences ( 12 - 15 ). (pnas.org)
Detection3
- Results: A new scheme and new software for optimal detection of oligonucleotide hybridization targets common to families of aligned sequences is suggested and applied to aligned sequence variants of the complete HIV-1 genome. (sciweavers.org)
- Since most laboratories have the experience and equipment for RT-PCR, rather than NASBA, we have compared NASBA to the Enterovirus Consensus RT-PCR kit from Argene Biosoft for EV detection in clinical specimens. (asm.org)
- The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results. (elsevier.com)
Escherichia1
- We have studied two enzymes of a newly described family of dehydrogenases with high sequence homology, 1,2-propanediol oxidoreductase of Escherichia coli and alcohol dehydrogenase II of Zymomonas mobilis. (udl.cat)
Highly conserved2
- upper-case letters indicate highly conserved bases, i.e. the 'AUGG' sequence is constant or rarely, if ever, changes. (wikipedia.org)
- Yamashita A , Kawashita N , Kubota-Koketsu R , Inoue Y , Watanabe Y , Ibrahim MS , Highly conserved sequences for human neutralization epitope on hemagglutinin of influenza A viruses H3N2, H1N1, and H5N1: implication for human monoclonal antibody recognition. (cdc.gov)
Evolutionary3
- In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. (wikipedia.org)
- From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
- We anticipate that long-read sequencing technologies such as PacBio SMRT will allow for the assembly of multigene family clusters and serve to more accurately characterize patterns of gene copy variation in large gene families, thus revealing novel micro-evolutionary patterns within non-model organisms. (duhnnae.com)
Hepatitis C vir1
- Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database. (mysciencework.com)
PacBio1
- Vol 15: The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. (duhnnae.com)
Species8
- These results show that wheat consensus primer sets can be used to isolate orthologous sequences, especially from species that are used for alien gene transfer in wheat. (kuleuven.be)
- We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. (plos.org)
- The population structure of L . calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. (plos.org)
- In addition, population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals representing diverse geographic locations stretching from North-Western India across South-East Asia and Australia to Papua New Guinea. (plos.org)
- Ancient DNA sequences have been retrieved from only a few fossils older than 100,000 years, but such DNA sequences can be tremendously useful in determining how different species are related to each other. (elifesciences.org)
- These sequences were analysed to determine how straight-tusked elephants are related to the three living elephant species and the extinct mammoth, the DNA sequences for which can be found in public databases. (elifesciences.org)
- Future research should include obtaining DNA sequences from additional extinct elephant species as well as careful re-evaluation of skeletal measurements for reconstructing elephant evolution. (elifesciences.org)
- The origin sequences vary across species, but all bacterial oriCs contain the information necessary to guide assembly of the DnaA protein complex at oriC , triggering the unwinding of DNA and the beginning of replication. (frontiersin.org)
Variant5
- Understanding the expected variant density of these regions and our ability to sequence them are therefore important considerations for designing future capture experiments. (biomedcentral.com)
- Hi, I tried to call variant for creating consensus sequence with the following command: samtools. (biostars.org)
- I downloaded a fasta file with a consensus sequence and a vcf file with the variant for certain i. (biostars.org)
- A second variant, 45-46m7, designed to thwart HIV-1 resistance to NIH45-46 G54W arising from mutations in a gp120 consensus sequence, targets a common route of HIV-1 escape. (rupress.org)
- Efforts to increase the diversity of sequencing data available for variant analysis are critical for accurate genetic diagnosis. (lww.com)
Molecular3
- Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. (springer.com)
- Nikiforova, Marina N. / Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels : A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists . (elsevier.com)
- Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. (biomedcentral.com)
Loci3
- This communication describes the consensus multi-locus typing scheme established by the Cryptococcal Working Group I (Genotyping of Cryptococcus neoformans and C. gattii) of the International Society for Human and Animal Mycology (ISHAM) using seven unlinked genetic loci for global strain genotyping. (nih.gov)
- Enrichment of loci by DNA hybridization-capture, followed by high-throughput sequencing, is an important tool in modern genetics. (biomedcentral.com)
- Microsatellites, or simple sequence repeats, are genetic loci where several nucleotide bases are repeated in tandem. (uga.edu)
Bcftools consensus1
- you could also give bcftools consensus a try. (biostars.org)
Mutation3
- In the current study, we examined the quality of protein single- point mutations in the OMIM and identified whether the corresponding reference sequences align with the mutation positions. (bvsalud.org)
- Our results show that close to 20% of mutation data cannot be mapped to a single reference sequence. (bvsalud.org)
- A new beta-thalassemia mutation produced by a single nucleotide substitution in the conserved dinucleotide sequence of the IVS-I consensus acceptor site (AG----AA). (biomedsearch.com)
Analysis13
- The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. (springer.com)
- This article includes an introduction to accessing the many suites of programs for analysis of protein structure, signatures of protein families, and consensus sequences that may be carried out on the internet. (springer.com)
- The generation of consensus sequences has been subjected to intensive mathematical analysis . (biology-online.org)
- CSIRO Entomology 120 Meiers Road Indooroopilly, Qld 4068, Australia) for providing the consensus sequences in the genetic divergence analysis. (thefreedictionary.com)
- Construction and Analysis of a Consensus Sequence. (pnas.org)
- The analysis of a data set from a previously published experimental phylogeny demonstrates the accuracy of the strict mutational compatibility consensus tree building method and illustrates its potential for obtaining unambiguous and precise results with full resolution. (biomedcentral.com)
- Mutational analysis pinpointed ribonucleotide sequences critical for binding. (mendeley.com)
- One of the most BLAST/) search analysis on 10, 2010, public health authorities essential features of this protocol was sequences obtained from the fi rst recognized 1,805 cases of pandemic strengthening laboratory capacity for cases identifi ed indicated the highest (H1N1) 2009 in Cuba. (cdc.gov)
- A small automaton for word recognition in DNA sequences and its application to consensus analysis of regulatory elements in DNA regions controlling gene expression. (edu.au)
- A method for pattern analysis of DNA sequence data is considered. (edu.au)
- Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. (biomedcentral.com)
- 2006. Sequencing for quasispecies analysis was done using the method described by Ramachandran et al. (cdc.gov)
- 0 denotes a consensus sequence with no quasispecies analysis. (cdc.gov)
Gene promoters1
- Sequence-specific transcription factor that binds gene promoters and activates their transcription. (genecards.org)
Mutational1
- As an alternative to such methods, a strict mutational compatibility consensus tree building method as a universally applicable and reliable method is reported. (biomedcentral.com)
Tumor1
- This webinar will demonstrate how clinical laboratories can develop their own customized targeted next-generation sequencing (NGS)-based solid tumor panels. (genomeweb.com)
Homologous1
- The general strategy of current character-based methods for an appropriate tree reconstruction from a homologous sequence set relies in the first place on an assumed tree for a given set of taxa. (biomedcentral.com)
Oligonucleotide1
- To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and Mcm2p binding sites at high resolution. (biomedcentral.com)
Regulatory sequences1
- We explore different sets of regulatory sequences to illustrate the performance of this method. (edu.au)
Mutations3
- Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus subtilis AddAB enzyme activities. (asm.org)
- An in vitro fluorescence polarization assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. (biomedcentral.com)
- A study that found multiple minority patients had previously been given positive results for the risk for hypertrophic cardiomyopathy on the basis of genetic mutations subsequently known to be benign elicited discussion among neurogeneticists about the importance of sequencing more diverse populations. (lww.com)
Genome-wide1
- We present, to our knowledge, the first genome-wide sequence data from eight individuals associated with archaeological remains from farming cultures in the El Portaln cave (Atapuerca, Spain). (scribd.com)
Bioinformatics1
- Bioinformatics tools are able to calculate and visualize consensus sequences. (wikipedia.org)
Amino acids3
- Although a consensus sequence was found in case of PSA-C1 clones with high frequency, this corresponds only in two amino acid positions with PSA (amino acids 9-15), and two amino acids were of similar physicochemical characteristics (W vs Y). (thefreedictionary.com)
- The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest [3] that this region has structural or functional importance. (wikipedia.org)
- The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)
Fasta5
- Dear all, I am trying to convert a BAM file containing aligned reads into a consensus fasta in o. (biostars.org)
- The fasta sequence does not match the REF at XLOC_000009.TCONS_00000016:733. (biostars.org)
- Hello, I'm trying to get a consensus fasta file using a Reference.fa and a Vcf.gz. (biostars.org)
- Hello everyone, I am trying to index a `.vcf.gz` file in order to get a fasta consensus with `b. (biostars.org)
- Hi I already used the following command to extract sequence from fasta file by IDs list. (biostars.org)
Generate4
- Hi everyone, I want to generate diploid consensus sequence for one human individual from BAM file. (biostars.org)
- Hi everyone, I want to generate polyploid consensus sequence for wheat from BAM file for purpose. (biostars.org)
- I am using samtools/bcftools to generate a 'de novo' consensus assembly for use with rc454 to cle. (biostars.org)
- Hello, I have been trying to generate a consensus sequence with samtools/bcftools for a couple o. (biostars.org)
Transposon1
- DNA transposon - consensus sequence. (girinst.org)
Circular consensus1
- Results: We generated 34,088 high quality circular consensus sequences of two diverse V1R subfamilies here referred to as V1RI and V1RIX from two individuals of Microcebus murinus. (duhnnae.com)
Primers2
- Significant DNA sequence variation between wheat and rye sequences in the non-coding regions was found, and this was used to develop seven sequence-specific primers. (kuleuven.be)
- The nested PCR primers used to isolate HCV sequences were designed and manufactured within CDC. (cdc.gov)