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.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
General agreement or collective opinion; the judgment arrived at by most of those concerned.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
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.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
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.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Nucleic acid sequences involved in regulating the expression of genes.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The functional hereditary units of BACTERIA.
Proteins found in any species of bacterium.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Proteins prepared by recombinant DNA technology.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
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.
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.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The relationships of groups of organisms as reflected by their genetic makeup.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Deletion of sequences of nucleic acids from the genetic material of an individual.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
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.
An iterative questionnaire designed to measure consensus among individual responses. In the classic Delphi approach, there is no interaction between responder and interviewer.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
Any method used for determining the location of and relative distances between genes on a chromosome.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
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 used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
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)
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.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
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.
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.
Transport proteins that carry specific substances in the blood or across cell membranes.
The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.
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.
Two-dimensional separation and analysis of nucleotides.
The rate dynamics in chemical or physical systems.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
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)
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).
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A proprotein convertase with specificity for the proproteins of PROALBUMIN; COMPLEMENT 3C; and VON WILLEBRAND FACTOR. It has specificity for cleavage near paired ARGININE residues that are separated by two amino acids.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
The functional hereditary units of FUNGI.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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 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.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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)
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.
Genotypic differences observed among individuals in a population.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
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.
An interferon regulatory factor that represses transcription of TYPE I INTERFERONS and activates transcription of HISTONE H4.
A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.
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)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
Ribonucleic acid that makes up the genetic material of viruses.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
Sequential operating programs and data which instruct the functioning of a digital computer.
Proteins found in any species of virus.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
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.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
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).
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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).
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
A protein which is a subunit of RNA polymerase. It effects initiation of specific RNA chains from DNA.
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.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The functional hereditary units of VIRUSES.
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.
The sum of the weight of all the atoms in a molecule.
Proteins found in any species of fungus.
A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Actual loss of portion of a chromosome.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The process by which a DNA molecule is duplicated.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
Proteins obtained from ESCHERICHIA COLI.
An interferon regulatory factor that binds upstream TRANSCRIPTIONAL REGULATORY ELEMENTS in the GENES for INTERFERON-ALPHA and INTERFERON-BETA. It functions as a transcriptional activator for the INTERFERON TYPE I genes.
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.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
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.
A family of SERINE ENDOPEPTIDASES isolated from Bacillus subtilis. EC 3.4.21.-
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
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.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
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 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.
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.
Proteins which are synthesized in eukaryotic organisms and bacteria in response to hyperthermia and other environmental stresses. They increase thermal tolerance and perform functions essential to cell survival under these conditions.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
A species of gram-positive bacteria that is a common soil and water saprophyte.
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)
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
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.
Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.
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.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
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.
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).
CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein.
The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.
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.
Societies whose membership is limited to physicians.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.
The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.
A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.
Viruses whose hosts are bacterial cells.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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).)
The process by which two molecules of the same chemical composition form a condensation product or polymer.

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)

Transcription factor p53 regulates its target genes through binding to DNA consensus sequence and activating the promoters of its downstream genes. The conventional p53 consensus binding sequence was defined as two copies of the 10-bp motif 5-PuPuPuC(A/T)(T/A)GPyPyPy-3 with a spacer of 0 to 13 bp, which exists in the regulatory regions of some p53 target genes. However, there is no such p53 cons
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Thus, terms like natural laws or phenomena in complex, probabilistic fields should have significantly less force: they are less laws or phenomena of nature than they are laws or phenomena of a statistical, simulacrum account of observations of nature.. Similarly, defining a product of nature is also often an exercise in probabilism, complicated by natural complexity. What scientists refer to as a typical human gene, for example, actually encompasses a wide variety of genetic sequences within the human population.184 Determining the archetypal sequence of that gene, the consensus sequence, is therefore very much a product of statistics, rather than the specific identification of a gene with the consensus sequence as it actually exists in nature.185 Characterizing a particular genetic sequence as a natural product is consequently a two-step act of probabilism: using statistical methodology to determine a consensus sequence, and then using statistical methodology to ...
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
CLUSTAL W (1.82) multiple sequence alignment consensus_2681#0 ---ATTTCCATTTTCATCGGCCTCGTATCTTGAAAGATATACAAAGTAAGAAAAAAATTT 57 consensus_2681#1 GGGATCACTGACTT-ACTTTAAAAGCATCTAGGTTATTGCGTTGACCGATAAATTATGTA 59 ** * ** * * **** * * * * *** * * consensus_2681#0 TATTAAAAAAAAGATAAGGACAAAGAA-ATTGTTGCTCACTTAACAGAAATGGGAAGACC 116 consensus_2681#1 AAATAATTAAGAAGTGTGAATATGAAATATCGATAAAATTTTTGTTAAAA-GAGATCATG 118 * *** ** * * * * * ** ** * * ** *** * ** * consensus_2681#0 TTCGGGGCTTTTATAAGAGAAGCTTCCTTTTACAGTTCGCACT----AGTTCACCGTCCA 172 consensus_2681#1 ATGTTGAATTGTGAGAAAAAATTTATAATTCAAAATTTACTTTTTGAAATATAAGATCAA 178 * * ** * * * ** * ** * * ** * * * * * ** * consensus_2681#0 CTAATTTCAGCATTTCCGTTTCCTCTTTTTGCACGTTATTCACCGGTGCATTTACATTTG 232 consensus_2681#1 CAAA---AAATATTTTTATCCAAAATATTAAAGCATTGAAAGCTG----AATTAGAAGTA 231 * ** * **** * * ** * ** * * * *** * * consensus_2681#0 AAATCGGACGATTCCTGGCTTTATTGTCCTCGAAGGGCGTATTCAAGATCAATCCACCAG 292 consensus_2681#1 ...
This would be trouble if we merged it as-is: it changes networkstatus_compute_bw_weights_v10, which is invoked from networkstatus_compute_consensus. We need all the authorities who are using the same consensus_method to produce the same output for the consensus, or else it wont be a consensus ...
Collaboration practically does not exist without consensus, and consensus happens with collaboration. Consensus is give-and-take in information sharing. Its the ability to discuss differences calmly and come to some form of an agreement. By discussing
Hello, We are in need of software, preferably free of charge or not too expensive, with which we can make alignments of our forward and reverse ABI trace files and build consensus sequences. Anybody with suggestions? H at ns ...
No abstract is available; but the full text article can be downloaded by clciking on the link on the right side. This article can be cited as: R. Egel, On the Misgivings of Anthropomorphic Consensus Polling in Defining the Complexity of LifeJ. Biomo
Alnylams third quarter 2013 loss of 48 cents per share was wider than the Zacks Consensus Estimate of a loss of 38 cents per share.
AIDS has emerged as a significant pediatric disease with the rate of infection in neonates born to HIV-infected mothers reported to be from 20- 50%. The clinical disease that occurs in HIV-infected infants is similar to the adult, although pediatric AIDS has a more rapid clinical course with a higher rate of mortality. About one-third of HIV-infected infants have a rapidly fatal disease course and die within l year; remaining infants develop clinical disease more slowly and survive for more than five years. The timing of vertical transmission, levels or type of maternal antiviral antibodies and, transmission of distinct maternal viral variants have been proposed to explain this bimodal pattern of disease progression, with the more rapid, severe outcome associated with prenatal infection, and due to transmission of highly pathogenic virus strains. HIV-infected children are frequently small-for-gestational-age or growth- restricted, and continue to exhibit poor weight gain and growth throughout ...
The Kozak consensus sequence, Kozak consensus or Kozak sequence is a sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG. The Kozak consensus sequence plays a major role in the initiation of the translation process. The sequence was named after the person who brought it to prominence, Marilyn Kozak. The sequence is identified by the notation (gcc)gccRccAUGG, which summarizes data analysed by Kozak from a wide variety of sources (about 699 in all) as follows: a lower-case letter denotes the most common base at a position where the base can nevertheless vary; upper-case letters indicate highly conserved bases, i.e. the AUGG sequence is constant or rarely, if ever, changes, with the exception being the IUPAC ambiguity code R which indicates that a purine (adenine or guanine) is always observed at this position (with adenine being claimed by Kozak to be more frequent); and the sequence in parentheses (gcc) is of uncertain significance. Kozaks paper was limited to a ...
Abstract:. Previous works from our laboratory demonstrated that the monoclonal antibody (MAb) called R7B4 is directed to an epitope shared by various receptors corresponding to the type I cytokine receptor family, containing the common motif WSXWS or the homologous F(Y)GEFS. Later a consensus peptide significantly recognized by the MAb was identified and synthesized (sequence HGYWSEWSPE). In the present work, an homologous of the consensus sequence (HHGYWSEWSPE) was conjugated to PADRE adjuvant to produce Ab that could simulate the MAb activity, that is, acting as hormone and/or cytokine antagonists. The covalently conjugated peptide-PADRE was a better immunogen than the consensus peptide alone according to the reactivity of sera from C57BL/6 immunized mice and, besides, no Ab to PADRE were detected. Furthermore, Ab to consensus peptide elicited after peptide-PADRE inoculation into mice behaved as immunomodulatory agents, since they improved the humoral response to a foreign antigen (in this ...
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation , 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution ...
The consensus layer defines cryptographic commitment structures. Its purpose is ensuring that anyone can locally evaluate whether a particular state and history is valid, providing settlement guarantees, and assuring eventual convergence. The consensus layer is not concerned with how messages are propagated on a network. Disagreements over the consensus layer can result in network partitioning, or forks, where different nodes might end up accepting different incompatible histories. We further subdivide consensus layer changes into soft forks and hard forks. ...
The CCDS database identifies a core set of human protein coding regions that are consistently annotated by multiple public resources and pass quality tests.
The CCDS database identifies a core set of human protein coding regions that are consistently annotated by multiple public resources and pass quality tests.
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination by Tyler Durden Dec 7, 2017 5:13 AM In the last 36 hours, Bitcoin has blasted through $12,000, $13,000, $14,000, and now $15,000 levels in an unprecedented 28% surge...
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination by Tyler Durden Dec 7, 2017 5:13 AM In the last 36 hours, Bitcoin has blasted through $12,000, $13,000, $14,000, and now $15,000 levels in an unprecedented 28% surge...
'Appallingly unmusical,' 'hirsute' and 'destined to fade away' - that pretty much sums up the general consensus.
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include the extensive range of known phosphorylation site motifs for protein kinase
Read Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close derivatives of the SA11-H96 strain, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Transcriptional repressor with bimodal DNA-binding specificity. Represses transcription in a methyl-CpG-dependent manner. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5-CGCG-3 but can also bind to the non-methylated consensus sequence 5-CTGCNA-3 also known as the consensus kaiso binding site (KBS). Can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA (PubMed:16354688 ...
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I want to pause here and talk about this notion of consensus, and the rise of what has been called consensus science. I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because youre being had ...
Something elese comes into my mind: Do you have ribosome biding site , (Kozak consensus element, reads gccaccaccATGg or similar) in your , construct? Not sure if applicable: Do you get expression, when you , transfect the construct in cells? Yes, there is a ribosome binding site (luciferase ATG translation start site). Although the flanking sequence surrounding the ATG may not be the optimal Kozak consensus sequence. I have not tried in-vivo transformation yet, but considering my in-vitro results I would expect the same results ...
Type: HE alpha-beta. Class of length: 4. Class: 4.1 , Consensus Ramachandran - aappplbb Subclass: 4.1.1 , Consensus Sequence - pphpXGpV. ...
We investigate to what extent the market uses information that is predictive of whether earnings will meet or beat the analyst consensus forecast of earnings (M
Cel-Sci Corporation with ticker code (CVM) have now 1 analysts in total covering the stock. The consensus rating is Buy. The target price ranges between
The idea behind Copenhagen Consensus 2012 is to prioritize some of the worlds most important spending, with the latest economic analysis providing us ...
Italian lawmakers will begin voting on Thursday to elect a new president, in the hope that they can end the countrys political impasse, over which concerns are growing.
Start End Score Size Count Identity Consensus 109775 110239 158 93 5 77.0 gactccatctcggactccaactcgggtccatctcgggtcctacttgggctccatttcggactccatctcgg actccatctcgggtccatctcg 116809 117552 142 186 4 72.0 gtcaaagtgggaatttgtacaaagccatgaagatgttcgattggatgccagacaagaatttgatctcatgg aactcaattctaagagcctttgctcatcatgggcaacttgacgaagcaaagatattatttgataaaatgcc cgagtgggacctaatgtcgttgaattcaatgcttgcggcatata 117603 118253 106 93 7 65.3 cctgagcgaaatcttgtttcttggaacgctatgcttgcagcatatgctcaacatgggcatattgaagatgc aaaggtgctgtttgataacatg 34251 34462 104 106 2 99.5 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna 32398 32553 71 39 4 85.3 actctccaacttactttgattcatcgcagtagctccatc 19938 20059 47 61 2 94.3 accgaaacacatcaagaaaaggaagacctcgaaactaggattgatagaacaagagctcacc 5405 5500 42 32 3 88.5 cgcaagaacaacaccatgaatcgcaaagaaaa 109582 109773 38 96 2 84.9 ggcctcggtctcggtctcggtcccgatctcggtctcggtctcggtctcggtcccggtctcggtctcgactt cggactccatctcggactccatctc 113787 114065 34 93 3 72.8 ...
Recent fate-mapping studies establish that microglia, the resident mononuclear phagocytes of the CNS, are distinct in origin from the bone marrow-derived myeloid lineage. 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. However, little is known about its roles in microglia. The CNS tissues of IRF8-deficient mice were immunohistochemically analyzed. Pure microglia isolated from wild-type and IRF8-deficient mice were studied in vitro by proliferation, immunocytochemical and phagocytosis assays. Microglial response in vivo was compared between wild-type and IRF8-deficient mice in the cuprizon-induced demyelination model. Our analysis of IRF8-deficient mice revealed that, in contrast to compromised development of IRF8-deficient bone marrow myeloid lineage cells, development and colonization of microglia are not obviously affected by loss of IRF8. However, IRF8
Rabbit anti IRF8 antibody recognizes Interferon regulatory factor 8, (IRF8) also known as Interferon consensus sequence-binding protein (I
The leader-following consensus problem of higher order multiagent systems is considered. The dynamics of each agent are given in general form of linear system, and the communication topology among the agents is assumed to be directed and switching. To track the leader, two kinds of distributed observer-based consensus protocols are proposed for each following agent, whose distributed observers are used to estimate the leader’s state and tracking error based on the relative outputs of the neighboring agents, respectively. Some sufficient consensus conditions are established by using parameter-dependent Lyapunov function method under a class of directed interaction topologies. As special cases, the consensus conditions for balanced and undirected interconnection topology cases can be obtained directly. The protocol design technique is based on algebraic graph theory, Riccati equation, and Sylvester equation. Finally, a simulation example is given to illustrate our obtained result.
Winterling KW, Chafin D, Hayes JJ, Sun J, Levine AS, Yasbin RE, Woodgate R (1998) The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J Bacteriol 180:2201-11.[PMID:9555905 ...
Probab=100.00 E-value=0 Score=636.12 Aligned_cols=238 Identities=42% Similarity=0.741 Sum_probs=223.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 99999999831231023222212468888751248999999999999999999999748999999999995302022433 Q gi,254780372,r 4 YCFFALFLVTPELVFAKSSLHDVMNIPADLSISTWIVRTFGIFTILSIAPILLIMVTCFPRFIIVFSILRTGMGMGSVPP 83 (246) Q Consensus 4 ~~~~~~~~~~~~~a~aq~~~~~~~~~~~~~~~~~~~iqll~llt~LsL~P~ilim~TsFtrIvIVLsilRnALG~QQ~PP 83 (246) T Consensus 140 ~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~q~~S~~iQ~Li~lT~LsllPaiLiM~TSFtRIvIVLslLRnALG~QQ~PP 219 (379) T PRK12430 140 IIPLCFLLLFCPSAYADIPGVTSHILSDGSQTWSIPVQTLVFLTSLTFLPAFLLMMTSFTRIVIVFGLLRNALGTPYAPP 219 (379) T ss_pred HHHHHHHHHHCHHHHHCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH T ss_conf 79799999967497853885215305899801230899999999999999999998520899999999987307688986 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf ...
This strategy guide introduces Consensus Decision Making, a method for facilitating and engaging students in a critical discussion of the central ideas of a text.
An organization headed by a senior IPCC official (Working Group 3 Vice-Chair, Carlo Carraro) has ranked TERI, an organization headed by the IPCCs chairman, first in the world ...
Uffe Ravnskov, MD, PhD is a Danish independent researcher and author.Famous for questioning the scientific consensus regarding the Lipid Hypothesis.
Curis reported fourth quarter 2013 net loss per share of 5 cents, narrower than the Zacks Consensus Estimate of a loss of 7 cents.
TSNAX Full-Length MS Protein Standard (NP_005990), Labeled with [U- 13C6, 15N4]-L-Arginine and [U- 13C6, 15N2]-L-Lysine, was produced in human 293 cells (HEK293) with fully chemically defined cell culture medium to obtain incorporation efficiency at Creative-Proteomics. This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs.
Downloadable (with restrictions)! In this paper we consider the dynamic process of race track betting. We show that there is a close connection between the dynamic race track betting process and the pari-mutuel method for constructing consensus of subjective probabilities considered in Eisenberg and Gale. This enables us to show that there exists a unique equilibrium point for the betting process. We further show that the dynamic betting process converges to this equilibrium point almost surely. Therefore the sequential race track betting gives a natural approach to inducing the consensus probabilities in Eisenberg and Gale. These consensus probabilities are different from the average of the subjective probabilities which is used in the conventional way of combining individually held opinions into a collective group statement. We compare these probabilities and this leads to a potential explanation of the favorite-longshot bias consistently observed in the studies of race track betting.
Diabetes has reached serious proportions and accounts for around 5% of the population of India. Its complications are the cause of tremendous socioeconomic problems.It is the single largest cause leading to atherosclerosis and its attendant complications such as heart attacks, strokes, paralysis, and non-healing ulcers of the foot
Diabetes has reached serious proportions and accounts for around 5% of the population of India. Its complications are the cause of tremendous socioeconomic problems.It is the single largest cause leading to atherosclerosis and its attendant complications such as heart attacks, strokes, paralysis, and non-healing ulcers of the foot
These oligonucleotides contain consensus DNA-binding sites for individual transcription factors and have 5´ OH blunt ends, allowing labeling to high specific activity with T4 PNK.
mouse Gbp3 protein: 71-kDa guanylate-binding protein; mGBP3 lacks CAAX consensus sequence for isoprenylation and methylation and thus is cytosolic, unlike other GBP3 proteins; RefSeq NM_018734
By using a consensus spot pattern in Delta2D (a), complete expression profiles (b) are generated. Profiles can be imported into DNA array analysis software (her
Is British Columbias carbon offset scheme really just a green slush fund - one in which the well-connected receive money that should have been spent on sick people ...
Synergy Pharma reported a loss of 17 cents per share in the fourth quarter, wider than the year-ago loss and the Zacks Consensus Estimate of a loss of 15 cents
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 ...
framing code (Trifonov 1987) The consensus sequence of the mRNA is (GCU)n which is complementary to (xxC)n in the ribosomes. It ... Trifonov had earlier discovered (GCU)n to be a hidden mRNA consensus sequence. Thus the combination of these two facts led them ... Finally, an ideal sequence of the nucleosomal DNA was derived in 2009 by Gabdank, Barash and Trifonov. The proposed sequence ... in RNA sequences RNA-to-protein translation code (triplet code) Every triplet in the RNA sequence corresponds (is translated) ...
... 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 ...
... the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number ... Family with sequence similarity 120 member A FAM122a: encoding protein Family with sequence similarity 122A FBP1 Fructose-1,6- ... 2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. doi:10.1038/nature02465. PMC 2734081. ... family with sequence similarity 73 member B FAM120A: ...
... the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number ... Family with sequence similarity 122 member B FAM122C: encoding protein Family with sequence similarity 122C FAM127A: CAAX box ... 2005). "The DNA sequence of the human X chromosome". Nature. 434 (7031): 325-37. doi:10.1038/nature03440. PMC 2665286. PMID ... evidenced from interspecies genomic sequence alignments. The X chromosome is notably larger and has a more active euchromatin ...
Warder DE, Keherly MJ (2004). "Ciz1, Cip1 interacting zinc finger protein 1 binds the consensus DNA sequence ARYSR(0-2)YYAC". ...
SUMOplot predicts the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot ... Users input a given an amino acid sequence into the web-enabled tool, and the program identifies internal sequences matching a ... Known autophagy receptors are characterized by short linear sequence motifs (autophagy receptor motifs, or ARMs) responsible ... The full sequence of the ARM-CP is displayed, where ARMs are colored by their score and ranked score-values are presented in ...
ABH08746 The query and the template sequences are aligned using a consensus alignment method. Different multiple sequence ... The consensus method is using a neural network to find the best aligned residues and analyzing all possible combinations using ... The usual four steps of homology modeling are executed: search for a template (similar sequence of known structure), align ... alignments are built using different alignment programs on two sets of sequences including the query and the template sequence ...
There are 3 consensus sequences for N-glycosylation and 1 chondroitin sulfate substitution site. The full blood count, ...
If the CPE has a consensus sequence, the presence of the PBE can double the resulting translational activation. The CPE is not ... The most common eCPE sequence is UUUUUUUUUUUU while the sequence of C-CPE is generally a very C rich region with the occasional ... While several sequence elements are known to regulate cytoplasmic polyadenylation, CPE is the best characterized. The most ... If the CPE has a nonconsensus sequence, a nearby Pumilio-binding element (PBE) is necessary for translational activation to ...
Hall SL, Padgett RA (1994). "Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites ... sequence) and U11 snRNA (matches the 5' sequence) as being putative factors involved in splicing of this new type of introns. ... they share only limited sequence homology (c. 40%). Furthermore, the sequence of U11 in comparison with U1, as well as U12 ... In 1994, S.L. Hall and R.A. Padgett compared the primary sequence of all reports on the four genes mentioned above. The results ...
Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the ... The splicing process itself is controlled by the given sequences, known as splice-donor and splice-acceptor sequences, which ... Mutations in these sequences may lead to retention of large segments of intronic DNA by the mRNA, or to entire exons being ... By comparing sequences with and without the splice site mutation, investigators were able to determine that a G-to-C nucleotide ...
The primary sequence of SPB components should contain consensus phosphorylation sites for mitotic kinases, because the SPB is ...
On the other hand, the attachment of a glycan residue to a protein requires the recognition of a consensus sequence. N-linked ... Oligosaccharyltransferase is the enzyme responsible for the recognition of the consensus sequence and the transfer of the ... side chain that is present as a part of Asn-X-Ser/Thr consensus sequence, where X is any amino acid except proline (Pro). In ... Asparagine must be located in a specific consensus sequence in the primary structure (Asn-X-Ser or Asn-X-Thr or in rare ...
T had the closest IR/DR sequence to the consensus sequence for the extinct Tc-1 like transposons in fish. The consensus ... 3). Each amino acid in the first completed transposase, called SB10, was determined by a "majority-rule consensus sequence" ... Further work has shown that the DNA-binding domain consists of two paired sequences, which are homologous to sequence motifs ... Although there were many sequences that looked like Tc-1 transposons in all the fish genomes studied, the transposon sequences ...
The absence of a glycosylation consensus sequence and the variability of glycan elaboration pose a challenge to studying O- ...
Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with ... Sequence databases: import, maintain, view, and export sequences. Multiple sequence alignment: align sequences of DNA, RNA, or ... Sequence alignment software Wright ES (2015). "DECIPHER: harnessing local sequence context to improve protein multiple sequence ... Analyze sequences: find chimeras, predict secondary structure, classify into a taxonomy, create phylogenetic trees, and ...
The N-terminal methionine is first cleaved by another enzyme and the X-Proline-Lysine consensus sequence is recognized by the ... The location of the modifications can be partially determined by DNA sequence, as well as small non-coding RNAs and the ... Narva, Kenneth E.; Van Etten, James L.; Slatko, Barton E.; Benner, Jack S. (1988-12-25). "The amino acid sequence of the ... Class C methylase has homologous sequence with the RS enzyme, coproporphyrinogen III oxidase (HemN), which also catalyzes the ...
The lacUV5 promoter sequence conforms more closely to the consensus sequence recognized by bacterial sigma factors than the ... Pribnow, D (1975). "Bacteriophage T7 Early Promoters: Nucleotide Sequences of Two RNA Polymerase Binding Sites". Journal of ...
Finally the sequence CAATC was identified as the consensus binding sequence for Quox1 homeodomain. By combining the power of ... Sequence the DNA: After final step of selection and electrophoresis, clone the DNA into a cloning vector and sequence it. ... It is also possible to identify the binding site even if both the protein and sequence is not known. Blackwell TK, Weintraub H ... We can apply the technique to less affinity binding sequence also, provided to keep high concentration of binding protein at ...
Novel consensus DNA-binding sequence for BRCA1 protein complexes». Mol. Carcinog. 38 (2): 85-96. PMID 14502648. doi:10.1002/mc. ... Zheng, L; Pan H, Li S, Flesken-Nikitin A, Chen P L, Boyer T G, Lee W H (2000). «Sequence-specific transcriptional corepressor ...
E.coli contains 9 bases of the 11 base consensus sequence in its oriC, within the 13-mer sequences. These sequences are found ... A general consensus sequence was made via comparison of conserved bacteria to form an 11 base sequence. ... In prokaryotes, DUEs are found in the form of tandem consensus sequences flanking the 5' end of DnaA binding domain. The act of ... No other sequence specificity involved in this interaction. Confirmed by inducing mutations along length of DUE-B sequence, but ...
Phrap uses Phred quality scores to determine highly accurate consensus sequences and to estimate the quality of the consensus ... to determine a sequence of base calls from the processed DNA sequence tracing: Predicted peak locations are determined, based ... Phrap was routinely used in some of the largest sequencing projects in the Human Genome Sequencing Project and is currently one ... The fluorescent-dye DNA sequencing is a molecular biology technique that involves labeling single-strand DNA sequences of ...
... take the form of single nucleotide polymorphisms in which a single nucleotide base is altered compared to a consensus sequence ... They can also exist as copy number variants (CNV) in which the copies of a gene or DNA sequence is different from the ... The human gene for the HGD nucleotide sequence shows a number of AKU-causing allelic mutations. Approximately 40 different ...
All of these receptors contain LIR consensus sequences that bind LC3/GABARAP which can lead to the degradation of the ... BNIP3 is then phosphorylated at its serine residues near the LIR sequence which promotes LC3 binding. FUNDCI is also hypoxia ... PINK1 contains a mitochondrial targeting sequence (MTS) and is recruited to the mitochondria. In healthy mitochondria, PINK1 is ...
No real ARE consensus sequence has been determined yet, and these categories are based neither on the same biological functions ... The best characterised adenylate uridylate (AU)-rich Elements have a core sequence of AUUUA within U-rich sequences (for ... Shaw G, Kamen R (August 1986). "A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA ... AREs have been divided into three classes with different sequences. ...
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. ... This sequence was originally called Box A, which is now known to be the sequence that interacts with the homologue of the ...
BvgR binds to a consensus sequence present within the coding sequences of at least some Bvg-repressed genes. Binding of this ... protein to the consensus sequence represents gene expression by reducing transcription. It is not known what the physiological ... Beattie D, Mahan M, Mekalanos J (1993). "Repressor binding to a regulatory site in the DNA coding sequence is sufficient to ... When phosphorylated, BvgA has increased affinity for specific binding sites in Bvg-activated promoter sequences and is able to ...
Dictyostelium class I and II share a consensus sequence (5'-CCUUACAGCAA-3') which is found in an 'open' area of the secondary ... Sequence Ontology page for Class II RNA Page for D. discoideum sRNA DdR35 at Rfam. ... This family was identified using shotgun sequencing of full-length cDNA libraries of small RNAs (sRNA) from the social amoeba ... an efficient search tool for fragmented patterns in genomic sequences". Genomics Proteomics Bioinformatics. 4 (1): 56-60. doi: ...
If a consensus base is covered by both high-quality sequence and (discrepant) low-quality sequence, Phrap's selection of the ... Phrap then assigns the confirmed base quality to the consensus sequence base. This makes it easy to (a) find consensus regions ... to determine the correct consensus sequence at all positions where the assembled sequences had discrepant bases. This approach ... Basically, at any consensus position with discrepant bases, Phrap examines the quality scores of the aligned sequences to find ...
2007). "The MN1 oncoprotein activates transcription of the IGFBP5 promoter through a CACCC-rich consensus sequence". J. Mol. ...
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- ...
"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 ...
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 ...
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". ...
... 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 ...
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 ...
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 ...
... 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 ...
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 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 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 ...
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 ...
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 ...
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 ...
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. ...
... 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] ...
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 ...
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 ...
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 ...
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. ...
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] ...
"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. ...
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. ...
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 ...
"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 ...
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. ...
The vast majority of animals and plants are able to synthesize vitamin C, through a sequence of enzyme-driven steps, which ... there is not consensus among countries. ... "Isolation and sequence analysis of a complementary DNA encoding ... "Phylogeny and Evolution of Selected Primates as Determined by Sequences of the ε-Globin Locus and 5′ Flanking Regions". ...
Consensus statement" (PDF). October 25-27, 2006. Arquivado dende o orixinal (PDF) o 09 de abril de 2008. Consultado o March 12, ... "An African HIV-1 Sequence from 1959 and Implications for the Origin of the epidemic". Nature 391 (6667): 594-7. Bibcode ...
184 Determining the archetypal sequence of that gene, the "consensus sequence," is therefore very much a product of statistics ... 185]. Thomas D. Schneider, Consensus Sequence Zen, 1 Applied Bioinformatics 111, 111, 113 (2002). ... methodology to subsequently determine whether the studied genetic sequence is similar enough to the consensus sequence to be ... the consensus sequence) with reality."188 Ultimately, if natural "laws," "phenomena," and "products" are "irreducibly ...
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 ...
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 ...
... 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 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.. 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 ...
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. 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 ...
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 ...
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/ . ...
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 ...
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.. 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 ...
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 ...
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 ...
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 ...
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 ...
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 ... 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 ...
... 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 ...
... 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 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 ... 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 ...
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 ...
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 ...
Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl Hi, I have a GATK vcf file and want to get the consensus sequence. I know ... Error in the creation of a consensus sequence from pileup Hello all, I want to create a consensus sequence from a Bam file I ... Generate Consensus sequence from BAM file Hi everyone, I want to generate diploid consensus sequence for one human individual ... poly ploid consensus seq generation Hi everyone, I want to generate polyploid consensus sequence for wheat from BAM file for ...
vcf-consensus outputs sequence same as reference I downloaded a fasta file with a consensus sequence and a vcf file with the ... Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl Hi, I have a GATK vcf file and want to get the consensus sequence. I know ... Get the consensus sequence ... (I know, should be easy) Hello, I have been trying to generate a consensus sequence with ... generating a reasonable consensus with bcftools + vcf-consensus Hi, I want to generate a consensus sequence using a bam ...
The applicability of consensus PCR primers across species and genera: the use of wheat Em sequences to develop markers for ... Two wheat consensus primer sets, directed to early-methionine-labelled (Em) gene sequences, were tested for their ability to ... These results show that wheat consensus primer sets can be used to isolate orthologous sequences, especially from species that ... Significant DNA sequence variation between wheat and rye sequences in the non-coding regions was found, and this was used to ...
... web server to manipulate multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence ... Posted by admin at 4:46 pm Tagged with: Consensus Sequence, Genome, GenomeCons, Sequence Alignments 50 views. Sorry, the ... GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences.. Sato T, Suyama M. ... GenomeCons 1.0 - Manipulate Multiple Genome Sequence Alignments and their Consensus Sequences. Alignment / BLAST ...
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • The transcription factor AtMYB2 binds to two sequence motifs in the promoter of the Arabidopsis ADH1 gene. (genetics.org)
  • At first sight this task might seem prohibitive, since the relevant upstream motifs are rather short sequences (in the range of 5 to 20 base pairs) to be found within hundreds or thousands of base pairs upstream of the coding region. (biomedcentral.com)
  • Common sequence motifs for protein, DNA, RNA, and small molecule S-adenosylmethionine-dependent methyltransferases. (ebi.ac.uk)
  • Klimasauskas S, Timinskas A, Menkevicius S, Butkiene D, Butkus V, Janulaitis A. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. (ebi.ac.uk)
  • Sequence analysis has identified three ATP-binding site consensus motifs. (ebi.ac.uk)
  • 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)
  • 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)
  • 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)
  • While many instances of this mechanism have been known in great detail for some time, it is only recently, thanks to the availability of several fully sequenced genomes and other experimental data on the scale of the entire genome, that a study of transcriptional regulation on a global scale has become possible. (biomedcentral.com)
  • 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)
  • We suggest in this review that, despite this diversity, a consensus bipartite motif can be identified. (nih.gov)
  • 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)
  • 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)
  • This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or more β-turns. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences [ PMID: 7897657 ]. (ebi.ac.uk)
  • 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)
  • 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)
  • The CCDS gene sets that have been arrived at by consensus of the different partners now consist of over 18,000 human and over 20,000 mouse genes (see CCDS release history). (wikipedia.org)
  • 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)
  • To solve this, we characterized differentially expressed genes (DEGs) in the whole blood of Dapulian (DPL) and Landrace piglets using RNA-seq (RNA-sequencing) technology. (hindawi.com)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • These include, but are not limited to: CACGTT sequence 20 bp upstream of the mouse Period2 (PER2) gene and regulates its expression CAGCTT sequence found within the MyoD core enhancer CACCTCGTGAC sequence in the proximal promoter region of human and rat APOE, which is a protein component of lipoproteins. (wikipedia.org)
  • 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)
  • 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)
  • Complementary sequences proximal to the 5′ and 3′ termini are predicted to direct cyclization of the (+)RNAs by forming panhandle structures from which short highly conserved terminal sequences protrude as single-stranded tails. (pasteur.fr)
  • 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)
  • samtools mpileup: bam file to consensus sequence generation error? (biostars.org)
  • 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)
  • 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)
  • Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is recognized and bound by transcription factors to initiate gene transcription. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. (springer.com)
  • Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. (springer.com)
  • CSIRO Entomology 120 Meiers Road Indooroopilly, Qld 4068, Australia) for providing the consensus sequences in the genetic divergence analysis. (thefreedictionary.com)
  • We established a genetic linkage map employing 518 simple sequence repeat (SSR, or microsatellite) markers for Bombyx mori (silkworm), the economically and culturally important lepidopteran insect, as part of an international genomics program. (semanticscholar.org)
  • Microsatellites, or simple sequence repeats, are genetic loci where several nucleotide bases are repeated in tandem. (uga.edu)
  • 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)
  • 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)
  • In our study, we employed long read sequencing combined with genetic and optical mapping, and syntenic information to produce a chromosomal level assembly. (plos.org)
  • 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)
  • Efforts to increase the diversity of sequencing data available for variant analysis are critical for accurate genetic diagnosis. (lww.com)
  • 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)
  • 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)
  • 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)
  • However, a region clearly related to exon 2 was identified in humans from its strong sequence homology to expressed exon 2 in other species. (mad-cow.org)
  • Exon 2 is changing very slowly in evolutionary time, with 6 species averaging 85% identity to a common ancestral consensus sequence some 100 million years back. (mad-cow.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • Vol 15: The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. (duhnnae.com)
  • 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 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)
  • 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)
  • Here, the authors generate a SOSIP trimer based on the consensus sequence of group M isolates, determine its structure and exposure of common epitopes, and show immunogenicity in rabbits and non-human primates. (nature.com)
  • 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)
  • The advent of next-generation sequencing (NGS) technology and progresses in bioinformatics have provided a useful platform to easily explore DEGs [ 5 ]. (hindawi.com)
  • Enrichment of loci by DNA hybridization-capture, followed by high-throughput sequencing, is an important tool in modern genetics. (biomedcentral.com)
  • Sequence-specific transcription factor that binds gene promoters and activates their transcription. (genecards.org)
  • 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)
  • 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)
  • This webinar will demonstrate how clinical laboratories can develop their own customized targeted next-generation sequencing (NGS)-based solid tumor panels. (genomeweb.com)
  • 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)
  • 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)
  • Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. (biomedcentral.com)
  • 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)
  • 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)
  • Very short or very similar sequences can be aligned by hand. (wikipedia.org)
  • however, there exist other E-boxes of similar sequences called noncanonical E-boxes. (wikipedia.org)
  • 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)
  • 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)
  • In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [ PMID: 2690010 ], although more conserved segments may be present. (ebi.ac.uk)
  • The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the alpha/beta core nucleotide-binding fold common to many kinases [ PMID: 8951040 ]. (ebi.ac.uk)
  • A "repeating sequence of nucleotides that forms a transcription or a regulatory signal" [1] is a box . (wikidoc.org)
  • 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)
  • Since the lexA box consensus sequence is only 16 bp, in order to clone it upstream the [bla. (thefreedictionary.com)
  • 1987). These sequences represent potential binding sites for Ste12p, the transcription factor that mediates pheromone-induced transcription, and are generally found upstream of pheromone-induced protein coding sequences (Kronstad et al. (nih.gov)
  • The general mechanism is fairly well understood, and involves the interaction between a trans-acting element, usually a protein, and a cis-acting element, a recognition site located upstream of the coding region of the regulated gene and consisting in a rather short DNA sequence to which the transcription factor is able to bind. (biomedcentral.com)
  • The BAC end sequences have been submitted to NCBI dbGSS under the accession numbers KS320706 - KS326261 for the Bam HI library and KS326262 - KS331896 for the Eco RI library. (plos.org)
  • Two wheat consensus primer sets, directed to 'early-methionine-labelled' (Em) gene sequences, were tested for their ability to amplify beyond their original source. (kuleuven.be)
  • Both primer sets fail to amplify Fm sequences from more distant monocots and the dicots. (kuleuven.be)
  • 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)