The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.
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.
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 order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
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 spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The 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.
Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.
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.
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
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)
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A 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.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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 multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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)
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The 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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
The functional hereditary units of BACTERIA.
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.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
The 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.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Proteins found in any species of bacterium.
The relationships of groups of organisms as reflected by their genetic makeup.
Ribonucleic acid that makes up the genetic material of viruses.
Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Established cell cultures that have the potential to propagate indefinitely.
The sum of the weight of all the atoms in a molecule.
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).
Proteins prepared by recombinant DNA technology.
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.
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.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
A 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.
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.
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).
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The rate dynamics in chemical or physical systems.
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)
Proteins found in any species of virus.
The functional hereditary units of VIRUSES.
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.
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.
Transport proteins that carry specific substances in the blood or across cell membranes.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Any method used for determining the location of and relative distances between genes on a chromosome.
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 single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
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.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
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.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
The 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.
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
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.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
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 most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
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.
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.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Sequential operating programs and data which instruct the functioning of a digital computer.
Proteins found in any species of fungus.
Family of RNA viruses that infects birds and mammals and encodes the enzyme reverse transcriptase. The family contains seven genera: DELTARETROVIRUS; LENTIVIRUS; RETROVIRUSES TYPE B, MAMMALIAN; ALPHARETROVIRUS; GAMMARETROVIRUS; RETROVIRUSES TYPE D; and SPUMAVIRUS. A key feature of retrovirus biology is the synthesis of a DNA copy of the genome which is integrated into cellular DNA. After integration it is sometimes not expressed but maintained in a latent state (PROVIRUSES).
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.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The functional hereditary units of FUNGI.
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.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
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.
Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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.
Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
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 serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
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.
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.
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.
Proteins obtained from ESCHERICHIA COLI.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
Viruses parasitic on plants higher than bacteria.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.
A 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).
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
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 complete genetic complement contained in a DNA or RNA molecule in a virus.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
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.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
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.
Two-dimensional separation and analysis of nucleotides.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
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.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
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.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Deletion of sequences of nucleic acids from the genetic material of an individual.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
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)
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The process of cleaving a chemical compound by the addition of a molecule of water.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.
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.
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Molecules of DNA that possess enzymatic activity.
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Viruses whose hosts are bacterial cells.
Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC
Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.
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.
A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.
Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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).
MOLECULAR BIOLOGY techniques used in the diagnosis of disease.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Viruses whose genetic material is RNA.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
A species of gram-positive bacteria that is a common soil and water saprophyte.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.
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.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
DNA or RNA bound to a substrate thereby having fixed positions.
Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.
Sites on an antigen that interact with specific antibodies.
The process by which a DNA molecule is duplicated.

Ultrabithorax function in butterfly wings and the evolution of insect wing patterns. (1/18435)

BACKGROUND: . The morphological and functional evolution of appendages has played a critical role in animal evolution, but the developmental genetic mechanisms underlying appendage diversity are not understood. Given that homologous appendage development is controlled by the same Hox gene in different organisms, and that Hox genes are transcription factors, diversity may evolve from changes in the regulation of Hox target genes. Two impediments to understanding the role of Hox genes in morphological evolution have been the limited number of organisms in which Hox gene function can be studied and the paucity of known Hox-regulated target genes. We have therefore analyzed a butterfly homeotic mutant 'Hindsight', in which portions of the ventral hindwing pattern are transformed to ventral forewing identity, and we have compared the regulation of target genes by the Ultrabithorax (Ubx) gene product in Lepidopteran and Dipteran hindwings. RESULTS: . We show that Ubx gene expression is lost from patches of cells in developing Hindsight hindwings, correlating with changes in wing pigmentation, color pattern elements, and scale morphology. We use this mutant to study how regulation of target genes by Ubx protein differs between species. We find that several Ubx-regulated genes in the Drosophila haltere are not repressed by Ubx in butterfly hindwings, but that Distal-less (Dll) expression is regulated by Ubx in a unique manner in butterflies. CONCLUSIONS: . The morphological diversification of insect hindwings has involved the acquisition of different sets of target genes by Ubx in different lineages. Changes in Hox-regulated target gene sets are, in general, likely to underlie the morphological divergence of homologous structures between animals.  (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (2/18435)

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

Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. (3/18435)

Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing approximately 5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus (ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met-hepatocyte growth factor receptor. The other cosmid contains only the two short 5'-most exons from the zinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the beta-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome.  (+info)

The mouse Aire gene: comparative genomic sequencing, gene organization, and expression. (4/18435)

Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and characterization of Aire, the murine ortholog of hAIRE. Comparative genomic sequencing revealed that the structure of the AIRE gene is highly conserved between human and mouse. The conceptual proteins share 73% homology and feature the same typical functional domains in both species. RT-PCR analysis detected three splice variant isoforms in various mouse tissues, and interestingly one isoform was conserved in human, suggesting potential biological relevance of this product. In situ hybridization on mouse and human histological sections showed that AIRE expression pattern was mainly restricted to a few cells in the thymus, calling for a tissue-specific function of the gene product.  (+info)

ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (5/18435)

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)

Cloning and functional characterization of the 5'-flanking region of the human bone morphogenetic protein-2 gene. (6/18435)

Bone morphogenetic protein-2 (BMP-2) is involved in bone formation, organogenesis or pattern formation during development. The expression of BMP-2 is regulated accurately and coordinately with that of other transforming growth factor-beta (TGF-beta) superfamily members. To elucidate the mechanism underlying the regulation of BMP-2 expression, a 6.7 kb SpeI-SalI fragment, from the P1 phage library, encompassing the 5'-flanking region of the human BMP-2 gene, was isolated and sequenced. Transcription start sites were mapped by the 5'-rapid amplification of cDNA ends (RACE) method. It has been found that the human BMP-2 gene contains, largely, two promoter regions surrounded by GC-rich sequences with several Sp1 consensus motifs. The proximal promoter possesses a single start site, whereas several start sites are clustered in the distal promoter region. Neither TATA nor CAAT consensus sequences are found in the proximity of the start sites for either promoter. Interestingly, in no case is the transcription-initiation site common between the human and mouse BMP-2 genes, although the sequence of the BMP-2 gene is well conserved in the promoter region between two species. Transient transfection experiments with the reporter fused with various lengths of the BMP-2 promoter sequence demonstrated that there exist enhancer elements in an 1.1 kb GC-rich fragment covering both promoter regions. It is noteworthy that the enhancer elements are 5'-flanked by a 790 bp strong repressor element that is characterized by numerous AT stretches. This intriguing organization may be amenable to the tight control of the expression of BMP-2 that is essential for development or bone morphogenesis.  (+info)

Use of RhD fusion protein expressed on K562 cell surface in the study of molecular basis for D antigenic epitopes. (7/18435)

The human D antigens, one of the most clinically important blood groups, are presented by RhD protein with a putative 12 transmembrane topology. To understand the molecular basis for the complex antigenic profile of RhD protein, we expressed a series of RhD fusion proteins using different portions of Duffy protein as a tag in erythroleukemic K562 cells. Because the reactivity of monoclonal anti-RhD antibody, LOR15C9, depends mainly on the sequence coded by exon 7 of RhD, we altered DNA sequence corresponding to the amino acid residues 323-331(A) and 350-354(B) in the exon 7. The mutation in region B resulted in a severe reduction in LOR15C9 binding by flow cytometry analysis, suggesting that region B may play an important role in constituting antigen epitopes recognized by LOR15C9. On the other hand, a slight decrease in the antibody binding was observed for the region A mutant, suggesting that the intracellularly located region A may elicit a long distance effect on the formation of exofacial antigen epitopes. In addition, using various monoclonal antibodies against RhD, we compared the antigenic profile of expressed RhD fusion protein with that of endogenous RhD in K562 cells as well as in erythrocytes.  (+info)

Suppression subtractive hybridization identifies high glucose levels as a stimulus for expression of connective tissue growth factor and other genes in human mesangial cells. (8/18435)

Accumulation of mesangial matrix is a pivotal event in the pathophysiology of diabetic nephropathy. The molecular triggers for matrix production are still being defined. Here, suppression subtractive hybridization identified 15 genes differentially induced when primary human mesangial cells are exposed to high glucose (30 mM versus 5 mM) in vitro. These genes included (a) known regulators of mesangial cell activation in diabetic nephropathy (fibronectin, caldesmon, thrombospondin, and plasminogen activator inhibitor-1), (b) novel genes, and (c) known genes whose induction by high glucose has not been reported. Prominent among the latter were genes encoding cytoskeleton-associated proteins and connective tissue growth factor (CTGF), a modulator of fibroblast matrix production. In parallel experiments, elevated CTGF mRNA levels were demonstrated in glomeruli of rats with streptozotocin-induced diabetic nephropathy. Mannitol provoked less mesangial cell CTGF expression in vitro than high glucose, excluding hyperosmolality as the key stimulus. The addition of recombinant CTGF to cultured mesangial cells enhanced expression of extracellular matrix proteins. High glucose stimulated expression of transforming growth factor beta1 (TGF-beta1), and addition of TGF-beta1 to mesangial cells triggered CTGF expression. CTGF expression induced by high glucose was partially suppressed by anti-TGF-beta1 antibody and by the protein kinase C inhibitor GF 109203X. Together, these data suggest that 1) high glucose stimulates mesangial CTGF expression by TGFbeta1-dependent and protein kinase C dependent pathways, and 2) CTGF may be a mediator of TGFbeta1-driven matrix production within a diabetic milieu.  (+info)

How closely related two or more separate strands of DNA are to each other, based on their base sequences. For more information, see homology. From the B...
I will describe a spectral sequence that starts at reduced odd Khovanov homology and converges to a version of instanton homology for double branched covers.. ...
Tätä artikkelia/julkaisua ei ole tallennettu Julkariin. Julkaisun tiedoissa voi kuitenkin olla linkki toisaalle tallennettuun artikkeliin/julkaisuun. ...
A review of the literature on homology indicates that the theory does not provide evidence for evolutionary naturalism, and that the common examples of homology can be better explained by Creation.
Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may represent homologies. See Reeck et al. (1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 60, 667 ...
Opens the Highlight Feature Bar and highlights feature annotations from the FEATURES table of the record. The Highlight Feature Bar can be used to navigate to and highlight other features and provides links to display the highlighted region separately. Links in the FEATURES table will also highlight the corresponding region of the sequence. More... ...
Page 1 of 4 - Vestigial Organs - posted in Best all time threads.: Most of the obvious anatomical homologies are between anatomical structures which are in active use by the species in question, but some anatomical homologies involve structures which are no longer needed but which also havent disappeared entirely. A vestigial organ or structure is any organ or structure found in a species which is not being used as it is in other species. Contrary to popular belief, vestigial organs a...
We will study the l1-homology of the 2-class in one relator groups. We will see that there are many qualitative and quantitive similarities between the l1-norm of the top dimensional class and the stable commutator length of the defining relation. As an application we construct manifolds with small simplicial volume.. This work in progress is joint with Clara Loeh.. ...
Considerable insights into important cis regulatory elements in a gene can be gleaned from the identification of sequence homologies among different species. To extend and optimize the sequence comparison between human and mouse erythropoietin (Epo) genes, we have obtained new human sequence from 5,547 to 385 bp upstream of the cap site and extended the 3 flank by 489 bp. In addition, we have obtained new sequence information on the mouse Epo gene extending from within the 3 untranslated region (UTR) to 1,001 bp downstream of the polyadenylation site. Analysis of these additional sequences shows considerable homology between human and mouse Epo genes as far as 4 kb (human) or 3 kb (mouse) upstream of the cap sites, as well as far more homology at the 3 end than was previously realized. In addition, both species were found to have a high frequency of short interspersed (SINE) repetitive sequences that interrupt homologies in both the 5 flank and within the transcription unit.
Knowledge of the sequence of a DNA segment has many uses, and some examples follow. First, it can be used to find genes, segments of DNA that code for a specific protein or phenotype. If a region of DNA has been sequenced, it can be screened for characteristic features of genes. For example, open reading frames (ORFs)-long sequences that begin with a start codon (three adjacent nucleotides; the sequence of a codon dictates amino acid production) and are uninterrupted by stop codons (except for one at their termination)-suggest a protein-coding region. Also, human genes are generally adjacent to so-called CpG islands-clusters of cytosine and guanine, two of the nucleotides that make up DNA. If a gene with a known phenotype (such as a disease gene in humans) is known to be in the chromosomal region sequenced, then unassigned genes in the region will become candidates for that function. Second, homologous DNA sequences of different organisms can be compared in order to plot evolutionary ...
NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997. />NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997. In the 1990s, the Ara Parseghian Foundation donated money to the National I. 0 Comments. ...
Marvin5.2 introduced the enumeration of homology groups. Homology groups are R-groups represented as pseudo atoms - with the names covering a set of R-groups either built-in or user-defined.. ...
package transeq import ( bufio bytes context encoding/binary fmt io runtime sync ) var ( letterCode = map[byte]uint8{ A: aCode, C: cCode, T: tCode, G: gCode, N: nCode, U: uCode, } standard = map[string]byte{ TTT: F, TCT: S, TAT: Y, TGT: C, TTC: F, TCC: S, TAC: Y, TGC: C, TTA: L, TCA: S, TAA: *, TGA: *, TTG: L, TCG: S, TAG: *, TGG: W, CTT: L, CCT: P, CAT: H, CGT: R, CTC: L, CCC: P, CAC: H, CGC: R, CTA: L, CCA: P, CAA: Q, CGA: R, CTG: L, CCG: P, CAG: Q, CGG: R, ATT: I, ACT: T, AAT: N, AGT: S, ATC: I, ACC: T, AAC: N, AGC: S, ATA: I, ACA: T, AAA: K, AGA: R, ATG: M, ACG: T, AAG: K, AGG: R, GTT: V, GCT: A, GAT: D, GGT: G, GTC: V, GCC: A, GAC: D, GGC: G, GTA: V, GCA: A, GAA: E, GGA: G, GTG: V, GCG: A, GAG: E, GGG: G, } ) ...
Definition of homologies in the Legal Dictionary - by Free online English dictionary and encyclopedia. What is homologies? Meaning of homologies as a legal term. What does homologies mean in law?
Sequencing: is the process of determining the nucleic acid sequence - the order of nucleotides in DNA. It includes any method or technology that is used
37 CFR 1.822(c)(5) provides that nucleotide sequences shall only be represented by a single strand, in the 5′ to 3′ direction, from left to right. That is, double stranded nucleotides shall not be represented in the sequence listing. A double stranded nucleotide may be represented as two single stranded nucleotides, and any relationship between the two may be shown in the drawings. The procedures for presenting and numbering amino acid sequences are set forth in 37 CFR 1.822(d). Two alternatives are presented for numbering amino acid sequences. Amino acid sequences may be numbered with respect to the identification of the first amino acid of the first mature protein or with respect to the first amino acid appearing at the amino terminal. The numbering procedure for nucleotides is set forth in 37 CFR 1.822(c)(6). Sequences that are circular in configuration are intended to be encompassed by these rules, and the numbering procedures described above remain applicable with the exception that the ...
The degree of similarity between sequences of Amino Acids. This information is useful for the analyzing genetic relatedness of Proteins and species ...
The observed gene overlays in the viruses ФX174 and SV40 show a surprising economy of information storage; two different amino acid sequences are read in different frames from the same stretch of DNA.
In article ,36nmhcINN2ng at, writes: , Hello, , Does anyone have any experience producing a very crude , structural hypothesis from sequence data? We have Sybyl, but Ive , been unable to get the Homology modeler to produce adequate results. , The situation is this: I have a sequence-structure coordinate file of , a protein with , 85 % homology to the protein I want to make a , structure for, but Sybyl complains about not having enough short , regions of homology! Are there any free programs that can do this? , Ive tried Sybyls built in structure-seq database, and constructed my , own database with many similar proteins and just the resolved protein , with homology. Any suggestions or references would be appreciated, , , Max Nanao , 95mhn at , nanao at Depends on what exactly is meant by , 85% homology (% sequence identity?), but, by most definitions of homology in most situations like this, you should not have a problem to calculate ...
M.P.E.P. Section 1823.02: Nucleotide and/or Amino Acid Sequence Listings, and Tables Related to Sequence Listings. Taken from the 9th Edition of the MPEP, Revision 08.2017, (Last Revised Jan. 2018). Updated in BitLaw in February 2018
No matter what the length of A and B are, A and B (the aligned sequences) will be of the same length. This simply comes from the definition of an alignment. The characters (representing base pairs) from the two sequences are arranged as to minimize the differences between them, and then the empty spaces (if any) are filled in with gaps (dash characters). These gaps are typically interpreted as evolutionary events between two homologous sequences, i.e. an insertion of nucleotides to one sequence or a deletion of nucleotides from the other (indels).. ...
Ordinary homology and cohomology factor through chain complexes via singular homology and cohomology. What about other (co)homology theories?. That is, for each spectrum $E$, do we have a lift in the following diagram?. $\begin{array}[ccc] & \mathsf{HoTop} & \overset{E}{\to} & \mathsf{GrAb} \\ & \underset{?}{\searrow} & \uparrow \\ & & \mathcal{D}(\mathsf{Ch}_{\mathbb{Z}}) \end{array}$. Where $\mathsf{HoTop}$ is the homotopy category, $E$ is $E$-homology or $E$-cohomology (in which case its contravariant, of course), $\mathsf{GrAb}$ is graded abelian groups, $\mathcal{D}(\mathsf{Ch}_{\mathbb{Z}})$ is the derived category of chain complexes in abelian groups, the functor $\mathcal{D}(\mathsf{Ch}_{\mathbb{Z}}) \to \mathsf{GrAb}$ is homology, and the functor labeled ? is the desired lifting.. It would just about suffice to do this in the universal example of stable homotopy (just about only because we have to do this for all spectra now), because we have a factorization:. $\begin{array}[ccc] & ...
Amino acid sequences of SsCOMT, SbCOMT, OsCOMT, TaCOMT, AtCOMT, and ZmCOMT were initially aligned by DNAMAN6.0 using default parameters, and followed by manual
The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36)
7800gccttctctg ccctgagggt cgaaggtcga gcaggccggg ggtgtccggg aggtctttgg 7860gcatcgcggt ctggggttgg gacgtgtaag cgcctgggag agcctagacc aggctccggg 7920ctgccaataa agaagtgaaa tgcgtatctg gtctcctgtc gtgggagagt gtgaggtgta 7980acggattcaa gtctgaaccc agagcctgga aaaggctgac cgcccagatt gacgttgcta 8040ggcaactccg gaggcgggcc cagcgccaaa agaacagggc gaggcgtcgt ccccgcatcc 8100cattggccgt tctctgcggg gccccgccct cgggggccgg agctagaagc tctacgcttc 8160cgaggcgcac ctcctggcct gcacgctttg acgt 8194162526DNAHomo sapiens 16atgctgctct gcacggctcg cctggtcggc ctgcagcttc tcatttcctg ctgctgggcc 60tttgcctgcc atagcacgga gtcttctcct gacttcaccc tccccggaga ttacctcctg 120gcaggcctgt tccctctcca ttctggctgt ctgcaggtga ggcacagacc cgaggtgacc 180ctgtgtgaca ggtcttgtag cttcaatgag catggctacc acctcttcca ggctatgcgg 240cttggggttg aggagataaa caactccacg gccctgctgc ccaacatcac cctggggtac 300cagctgtatg atgtgtgttc tgactctgcc aatgtgtatg ccacgctgag agtgctctcc 360ctgccagggc aacaccacat agagctccaa ggagaccttc tccactattc ccctacggtg 420ctggcagtga ttgggcctga cagcaccaac ...
Chalmers R, Sewitz S, Lipkow K, Crellin P. Complete nucleotide sequence of Tn10. J Bacteriol. 2000 May;182(10):2970-2. doi: 10.1128/jb.182.10.2970-2972.2000. PubMed ID: 10781570 ...
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Anyway, if you get some proteins, you identify them with mass spec (either MALDI or digest on LC-MS) and this information you use for the identification ...
human CSDE1 protein: amino acid sequence in first source; unr gene located close to N-ras locus and may interact with it; RefSeq NM_007158
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We have conducted a human cDNA project to predict protein-coding sequences (CDSs) in large cDNAs (, 4 kb) since 1994, and the number of newly identified genes, known as KIAA genes, already exceeds 2000. The ultimate goal of this project is to clarify the physiological functions of the proteins encoded by KIAA genes. To this end, the project has recently been expanded to include isolation and characterization of mouse KIAA-counterpart genes. We herein present the entire sequences and the chromosome loci of 500 mKIAA cDNA clones and 13 novel cDNA clones that were incidentally identified during this project. The average size of the 513 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 816 amino acid residues. By comparison of the predicted CDSs between mouse and human KIAAs, 12 mKIAA cDNA clones were assumed to be differently spliced isoforms of the human cDNA clones. The comparison of mouse and human sequences also revealed that four pairs of human ...
For the Predefined groups, the R-group definitions specify the enumerable library as User-defined groups. I.e. these groups definitions can be customized. These structures are characteristic to the Homology group and encompass simple and large structures as well.. We have to emphasize, that these definitions are used only for enumeration and do not affect searching. As noted earlier, arbitrary structures fulfilling the requirements for the Homology group will match such a target.. Enumeration definitions contain two attachment points as default. After enumeration these are the atoms which connect to the first two neighbors of the group. If the enumerated Homology groups Pseudo atom has more than two connections, then further attachment points are added. These are put on atoms that have free valence and comply the requirements for externally connecting atoms of the given group. E.g. for aryl only aromatic ring atoms can be the connection points. The atoms of the definition are investigated in ...
cloning of non-coding region for protein expression - posted in Protein Expression and Purification: Hi! I am trying to see the function of my non-coding region in protein expression. I have clone my gene and its non-coding region upstream of 5UTR to find if non-coding region plays any role in expression of cloned protein. I have other clones with no non-coding region just 5UTR and coding region. Has anybody cloned these type construct in mammalian expression vector and does...
Purchase Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 - 1st Edition. Print Book & E-Book. ISBN 9780121820848, 9780080883007
Genomic organization, chromosomal mapping, nucleotide sequence, and predicted amino acid sequence of the murine MCP-5 gene. (A) Partial restriction map and ge
Eiglmeier, K., W. Boos, S.T. Cole 1987. Nucleotide sequence and transcriptional startpoint of the glpT gene of Escherichia coli: extensive sequence homology of the glycerol-3-phos transport protein with components of the hexose-6-phos transport system ...
develop a new model summarizing the entire process of transcription and translation with your lab group you will be asked to communicate share amino acid sequence chart dna.. ...
This MATLAB function cuts SeqAA, an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or abbreviation code for an enzyme or compound for which the literature specifies a cleavage rule.
This MATLAB function cuts SeqAA, an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or abbreviation code for an enzyme or compound for which the literature specifies a cleavage rule.
I was wondering if I did something wrong with the deletion, it seems pretty self explanatory but I just want to make sure I did this right. The filled in answers are in bold And Im completely lost with the Amino Acid sequence, my TA did this in class and I still dont get it ...
The next few posts are presented to help you prepare for the AP exam. This first post addresses the homologies between humans and chimps. Recall that homologies are traits that are derived from the same ancestral form - they have a shared ancestry ...
lets assume that i fould a valuable gene fragment ex. dna sequence homology with one of the human myosin ii genes1., Hire Biology Expert, Ask Academics Expert, Assignment Help, Homework Help, Textbooks Solutions
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Extensive nucleotide sequence data is new known for six small isometric phages, ([o with diagonal slash]Xl 74, G4, St-1, Sl3, [lowercase alpha]3 and [phi]K).Comparison of these sequences allows us to observe the role of ...
Tsou, C.H., Li, L. & Vijayan, K. 2016. The Intra-familial Relationships of Pentaphylacaceae sl as Revealed by DNA Sequence Analysis. Biochemical Genetics pp.1-13. doi: 10.1007/s10528-016-9717-1 ...
Mc kean, D J.; Potter, M; and Hood, L, Amino acid sequence comparison of three new balb/c mouse kappa chains. Abstr. (1972). Subject Strain Bibliography 1972. 679 ...
TY - JOUR. T1 - Deduced primary structure of rat tryptophan-2,3-dioxygenase. AU - Maezono, Katsumi. AU - Tashiro, Kosuke. AU - Nakamura, Toshikazu. PY - 1990/7/16. Y1 - 1990/7/16. N2 - The complete amino acid sequence of the tryptophan 2, 3-dioxygenase (TO) of rat liver was determined from the nucleotide sequence of a full length TO cDNA isolated from a rat liver cDNA library and determined its primary structure. TO was encoded in a mRNA of about 1.7 kb containing an open reading frame of 1218 bp. According to the deduced amino acid sequence, the monomeric polypeptide of TO consisted of 406 amino acid residues with a calculated molecular weight of 47,796 daltons. It has twelve histidine residues around its hydrophobic region, which has homology with some heme proteins and oxygenase, suggesting that this hydrophobic region might to be the core of TO for the activity.. AB - The complete amino acid sequence of the tryptophan 2, 3-dioxygenase (TO) of rat liver was determined from the nucleotide ...
The full-length ORF clone contains only the coding sequence of the full-length protein, while the other full-length cDNA clones contain some untranslated sequences, such as the 5side or 3′ side non translation. It is well known that these untranslated sequences may have a negative effect on the transcription and translation processes of the encoded proteins in the host.. If it is the ORF expressed clone, it can be transfected into cells and expressed in cells.. In the general situation, the carrier of cDNA clone is not the expression vector, so it can not be directly used for transfection of cells.. The difference between ORF, cDNA and CDS:. 1.what is a full-length ORF clone?. A full-length ORF clone is a plasmid inserted into a DNA fragment encoding a full-length protein. The inserted DNA fragment only contains sequence incoding a full-length protein, and does not contain the untranslated region of 5 or 3 end (UTRs) or intron.. 2.why should the full length ORF cDNA clones are used instead ...
Read Hop mosaic virus: complete nucleotide sequence and relationship to other carlaviruses, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Chang, E., et al. N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis. Journal of Biomolecular Technology. 27(2). 07/03/2016.. ...
I) instructions for representing the set of sequence elements on a display, each sequence element representing an amino acid sequence segment or a nucleic acid sequence segment, wherein the set of sequence elements collectively encode the design nucleic acid sequence, wherein said instructions for representing said set of sequence elements comprise instructions for displaying a plurality of icons in a linear or a near linear arrangement on a display, each respective icon in said plurality of icons uniquely representing a corresponding sequence element in said set of sequence elements such that neighboring icons in said plurality of icons represent neighboring sequence elements in said plurality of sequence elements in said design nucleic acid sequence, and each said respective icon in said plurality of icons depicts a directional property for the corresponding sequence element in said set of sequence elements; and ...
Stanniocalcins (STCs) represent small glycoprotein hormones, found in all vertebrates, which have been functionally implicated in Calcium homeostasis. However, recent data from mammalian systems indicated that they may be also involved in embryogenesis, tumorigenesis and in the context of the latter especially in angiogenesis. Human STC1 is a 247 amino acids protein with a predicted molecular mass of 27 kDa, but preliminary data suggested its di- or multimerization. The latter in conjunction with alternative splicing and/or post-translational modification gives rise to forms described as STC50 and big STC, which molecular weights range from 56 to 135 kDa. In this study we performed a biochemical and structural analysis of STC1 with the aim of obtaining low resolution structural information about the human STC1, since structural information in this protein family is scarce. We expressed STC1 in both E. coli and insect cells using the baculo virus system with a C-terminal 6 × His fusion tag. From the
We previously reported the isolation and characterization of a cDNA clone, I-309, that encodes a small secreted protein produced by activated human T lymphocytes. This protein is structurally related to a large number of recently identified proteins that are secreted upon cellular activation. In this report we describe the isolation and characterization of the gene encoding I-309. The genomic organization is essentially identical to that found in the genes encoding the structurally similar proteins TCA-3, hJE/MCP-1, and mJE, strengthening the hypothesis that these genes are evolutionarily related. The region of the I-309 gene 5 of the mRNA cap site exhibits extensive nucleotide sequence homology with the same region of the murine gene TCA-3, providing additional evidence that I-309 and TCA-3 are likely to be homologs. Finally, panels of rodent-human somatic cell hybrids were used to map the I-309 gene to human chromosome 17. In conjunction with recent mapping data from other laboratories, this ...
Maloy W.L.; Nathenson S.G.; Coligan J.E., 1981: Primary structure of murine major histo compatibility complex allo antigens amino acid sequence of the amino terminal 98 residues of the h 2d b glyco protein
The distinct subcellular redistribution of p53 and p73 in MDM2-expressing cells suggests the existence of structural differences between the proteins. Whereas the oligermerization domain of p53 and p73 share 33% identity, the extreme CT (outside of the oligermerization domain) of the two proteins is much less conserved. Inspection of the primary amino acid sequence reveals that the p53 CT contains five lysine residues that are not conserved in p73. In addition, we showed recently that under conditions where p53 is highly ubiquitinated, p73 exhibits a much lower tendency for ubiquitination (10) . According to the current model of p53 nuclear export, the p53 NES is inactive when p53 is in tetramer. Ubiquitination of the p53 CT lysine residues by MDM2 results in the revealing of the NES that then permits p53 to be nuclear-exported (5, 6, 7) . It is therefore possible that the NES of p73 is unable to be activated because of its lack of the corresponding lysine residues available for ubiquitination. ...
Patenting around nuisance prior art. Patenting gene sequences. Patenting nucleotide and amino acid sequences in view of electronic sequence database searches
A RecA-single-stranded DNA (RecA-ssDNA) filament searches a genome for sequence homology by rapidly binding and unbinding double-stranded DNA (dsDNA) until homology is found. We demonstrate that pulling on the opposite termini (3′ and 5′) of one of the two DNA strands in a dsDNA molecule stabilizes the normally unstable binding of that dsDNA to non-homologous RecA-ssDNA filaments, whereas pulling on the two 3′, the two 5′, or all four termini does not. We propose that the outgoing strand in the dsDNA is extended by strong DNA-protein contacts, whereas the complementary strand is extended by the tension on the base pairs that connect the complementary strand to the outgoing strand. The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present ...
Ben Hanelt, D. Van Schyndel, C. M. Adema, L. A. Lewis, E. S. Loker. The Phylogenetic Position of Rhopaluva ophiocomae (Orthonectida) Based on 18s Ribosomal DNA Sequence Analysis. -Molecular Biology and Evolution, 1996,. 13 (9), lk 1187-1191. Veebiversioon. ...
Every protein in a cell is created through the transcription of a specific sequence, that is part of the DNA. This transcription provides the sequence in which amino acids are to be linked, to form a protein.
LBHD1 - C11orf48 (untagged)-Human chromosome 11 open reading frame 48 (C11orf48) available for purchase from OriGene - Your Gene Company.
Definition of primary structure - the characteristic sequence of amino acids forming a protein or polypeptide chain, considered as the most basic element of its str
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.
GLYATL1P1 (glycine-N-acyltransferase like 1 pseudogene 1), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
This page is meant to be a storage place for example data. Hopefully this example data will help people to learn how to use Mussa without going through the trouble of finding homologous regions in multiple species. ...
"The MPI Bioinformatics Toolkit as an Integrative Platform for Advanced Protein Sequence and Structure Analysis." Nucleic Acids ... Homology is the relationship between biological structures or sequences derived from a common ancestor. Homologous proteins ( ... Nucleic Acids Research 25.17 (1997): 3389-402. Oxford University Press. Print [4] Bigert, A., and J. Söding. "Sequence Context- ... The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. The query ...
Hloch P, Schiedner G, Stahl H (1990). "Complete cDNA sequence of the human p68 protein". Nucleic Acids Res. 18 (10): 3045. doi: ... Ford MJ, Anton IA, Lane DP (1988). "Nuclear protein with sequence homology to translation initiation factor eIF-4A". Nature. ... 2000). "Structure and expression of the human p68 RNA helicase gene". Nucleic Acids Res. 28 (4): 932-9. doi:10.1093/nar/28.4. ... Nucleic Acids Res. 31 (5): 1470-80. doi:10.1093/nar/gkg236. PMC 149829. PMID 12595555. Wilson BJ, Giguère V (2007). " ...
"The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... "The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... The introns were not placed randomly; they fell in the center of the region of amino acid sequence homology in strikingly ... Computer-assisted analysis of the internal homology in amino acid sequence suggested duplication of an ancestral gene thus ...
The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a ... The FALC-Loop web server for protein loop modeling" Nucleic Acids Research 39, W210-W214 (2011). Lee J, Lee D, Park H, Coutsias ... Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology" Structure 4: 1123-27 ... The extent of the inaccuracy increases with the number of amino acids in the loop. The loop amino acids' side chains dihedral ...
"Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.. ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. ...
Any algorithm that is designed for homology search of nucleic acid sequences can be used, e.g., BLAST. However, such algorithms ... Eddy SR, Durbin R (June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Res. 22 (11): 2079-2088. doi: ... Homology search refers to the process of searching a sequence database for RNAs that are similar to already known RNA sequences ... Tempel S, Tahi F (2012). "A fast ab-initio method for predicting miRNA precursors in genomes". Nucleic Acids Res. 40 (11): 955- ...
"Identification of two large subdomains in TFIIE-alpha on the basis of homology between Xenopus and human sequences". Nucleic ... Acids Res. 20 (21): 5838. doi:10.1093/nar/20.21.5838. PMC 334425. PMID 1454543. Heng HH, Xiao H, Shi XM, Greenblatt J, Tsui LC ... Sumimoto H, Ohkuma Y, Sinn E, Kato H, Shimasaki S, Horikoshi M, Roeder RG (1991). "Conserved sequence motifs in the small ... "Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE". Nature. 354 ...
... sequence homology with other human acute phase protein genes". Nucleic Acids Res. 13 (11): 3941-52. doi:10.1093/nar/13.11.3941 ... 1973). "Structure of 1 -acid glycoprotein. The complete amino acid sequence, multiple amino acid substitutions, and homology ... acid glycoprotein and the elucidation of the amino acid sequence of the carboxyl-terminal cyanogen bromide fragment". ... Board PG, Jones IM, Bentley AK (1986). "Molecular cloning and nucleotide sequence of human alpha 1 acid glycoprotein cDNA". ...
... "cDNA sequence of a new ras-related gene (rap2b) isolated from human platelets with sequence homology to rap2". Nucleic Acids ... The most striking difference between the RAP and RAS proteins resides in their 61st amino acid: glutamine in RAS is replaced by ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... The proteins encoded by these genes share approximately 50% amino acid identity with the classical RAS proteins and have ...
Coconuts from Asia and South Pacific have been found to have viroids with similar nucleic acid sequences of CCCVd. The ... Moreover, they share sequence homology with other viroids. Conditions for a viroid to infect its host include wounds on the ... The first step is the purification to obtain the nucleic acids of the plant cells. The leaves of the plant located four or more ... This viroid has 64% sequence homology with the cadang-cadang viroid. There are other related viroids with the CCCVd, which are ...
Venta PJ, Tashian RE (1990). "PCR detection of the TAQ1 polymorphism at the CA2 locus". Nucleic Acids Res. 18 (18): 5585. doi: ... 1988). "Cloning, expression, and sequence homologies of cDNA for human carbonic anhydrase II". Genomics. 1 (2): 159-66. doi: ... Nucleic Acids Res. 15 (11): 4687. doi:10.1093/nar/15.11.4687. PMC 340889. PMID 3108857. Murakami H, Marelich GP, Grubb JH, et ... Montgomery JC, Venta PJ, Tashian RE, Hewett-Emmett D (1987). "Nucleotide sequence of human liver carbonic anhydrase II cDNA". ...
Medema, Marnix H.; Takano, Eriko; Breitling, Rainer (2013-02-14). "Detecting Sequence Homology at the Gene Cluster Level with ... Tanako, Eriko (2013). "antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers". Nucleic Acids ... These can include the secondary biosynthetic pathways that have been identified from any genome sequence. Genome sequencing ... Nucleic Acids Research. 39 (Web Server issue): W339-W346. doi:10.1093/nar/gkr466. PMC 3125804. PMID 21672958. ...
Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... 1996). "Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology". Comput. Appl. ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834. PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, doi:10.2277/ ...
... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... Nucleic Acids Res. 39 (Web Server issue): W13-7. doi:10.1093/nar/gkr245. PMC 3125728. PMID 21558174. Kemena C, Notredame C ( ... In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can ... It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences ...
... which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3'". Nucleic Acids Res. 27 (13): 2644-5. doi:10.1093/nar/ ... Rina M, Markaki M, Bouriotis V (December 1994). "Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII ... and the discovery of a wrongly sequenced site in pACYC177". Nucleic Acids Res. 19 (9): 2321-3. doi:10.1093/nar/19.9.2321. PMC ... which recognizes the pentanucleotide sequence 5'-CTCAG(N)(10/8)". Nucleic Acids Res. 29 (4): 895-903. doi:10.1093/nar/29.4.895 ...
E6 is a 151 amino-acid peptide that incorporates a type 1 motif with a consensus sequence -(T/S)-(X)-(V/I)-COOH. It also has ... Coggins LW, Ma JQ, Slater AA, Campo MS (June 1985). "Sequence homologies between bovine papillomavirus genomes mapped by a ... Nucleic Acids Research. 20 (11): 2889. doi:10.1093/nar/20.11.2889. PMC 336941. PMID 1319576. Varsani A, Kraberger S, Jennings S ... Compared to other papillomavirus genes, the amino acid sequences of most portions of L1 are well-conserved between types. ...
Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ... coli protein sequences for homology in other genomes and find over 6000 pairs of sequences with shared homology to single ... August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi: ... Because the two sequences in each protein pair are non-homologous, these interactions could not be predicted using homology- ...
Nucleic Acids Research. 21 (16): 3719-23. doi:10.1093/nar/21.16.3719. PMC 309874. PMID 8396237. Nakano H, Yamazaki T, Miyatake ... complete coding sequence and homology with other type II topoisomerases". Biochimica et Biophysica Acta (BBA) - Gene Structure ... Nucleic Acids Research. 20 (21): 5587-92. doi:10.1093/nar/20.21.5587. PMC 334390. PMID 1333583. "Entrez Gene: TOP2B ... Ng SW, Liu Y, Schnipper LE (Dec 1997). "Cloning and characterization of the 5′-flanking sequence for the human DNA ...
Beintema JJ, Wietzes P, Weickmann JL, Glitz DG (Jan 1984). "The amino acid sequence of human pancreatic ribonuclease". ... Nucleic Acids Research. 20 (3): 612. doi:10.1093/nar/20.3.612. PMC 310435. PMID 1741299. Sakakibara R, Hashida K, Tominaga N, ... N-terminal sequence homology with human nonsecretory ribonuclease". Chemical & Pharmaceutical Bulletin. 39 (1): 146-9. doi: ... Haugg M, Schein CH (Feb 1992). "The DNA sequences of the human and hamster secretory ribonucleases determined with the ...
Nucleic Acids Research. 22 (4): 625-631. doi:10.1093/nar/22.4.625. PMC 307853. PMID 7510398. Turnbough CL, Switzer RL (2008). " ... "The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology ... This hairpin blocks ribosome-binding at the Shine-Dalgarno sequence, and therefore blocks expression of PyrD. Under low CTP/GTP ... Translation initiation can occur at more than one different site within this leader sequence, under high cytidine triphosphate ...
... probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. *^ Söding J (2005). "Protein homology ... sequences of S. {\displaystyle S}. until the modified sequences, S. i. ′. {\displaystyle S_{i}^{'}}. , all conform to length L ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' ...
WU virus was discovered by shotgun sequencing of the nucleic acids found in the respiratory secretions of a young patient ... Sequence homology was detected among the sequences found in the clinical sample and the known genomes of other human ... The complete genome of the WU virus has been sequenced and found to be a circular double-stranded DNA genome of 5229 base pairs ...
... sequence homology, amino acid MeSH G13.810.550 - sequence homology, nucleic acid MeSH G13.810.550.830 - synteny MeSH G13.920. ... sequence deletion MeSH G13.920.590.762.180 - chromosome deletion MeSH G13.920.590.762.320 - gene deletion MeSH G13.920.590.835 ...
Homology (biology) KEGG Multiple Sequence Alignment MicrobesOnline home page IMG home page reference: Nucleic Acids Research, ... A curated non-redundant sequence database of genomes, transcripts and proteins". Nucleic Acids Research. 35 (Database issue): ... Bates, J. T.; Chivian, D.; Arkin, A. P. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps". Nucleic Acids Research. ... Letunic, I.; Doerks, T.; Bork, P. (2009). "SMART 6: Recent updates and new developments". Nucleic Acids Research. 37 (Database ...
Homology search tools may take an individual nucleic acid or protein sequence as input, or use statistical models generated ... In coding sequences, the nucleic acid and amino acid sequence may be conserved to different extents, as the degeneracy of the ... The codon usage bias in some organisms may restrict the types of synonymous mutations in a sequence. Nucleic acid sequences ... Conservation can occur in coding and non-coding nucleic acid sequences. Highly conserved DNA sequences are thought to have ...
Edmonds, M (2002). A history of poly A sequences: from formation to factors to function. Progress in Nucleic Acid Research and ... and sequence homology with exosome proteins". The Plant Cell. 15 (9): 2003-19. doi:10.1105/tpc.013326. PMC 181327. PMID ... Tian B, Hu J, Zhang H, Lutz CS (2005). "A large-scale analysis of mRNA polyadenylation of human and mouse genes". Nucleic Acids ... Slomovic S, Laufer D, Geiger D, Schuster G (2006). "Polyadenylation of ribosomal RNA in human cells". Nucleic Acids Research. ...
Exploiting structure to help users understand their sequences". Nucleic Acids Research. 43 (Database issue): D382-6. doi: ... CS1 maint: discouraged parameter (link) Shi, J.; Blundell, T. L.; Mizuguchi, K. (2001). "FUGUE: Sequence-structure homology ... Sali, Andrej (1984). Modelling three-dimensional structure of a protein from its amino acid sequence. (PhD thesis ... Nucleic Acids Research. 45 (W1): W229-W235. doi:10.1093/nar/gkx439. ISSN 0305-1048. PMC 5793720. PMID 28525590. Blundell TL, ...
1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University ... Girdea, M; Noe, L; Kucherov, G (January 2010). "Back-translation for discovering distant protein homologies in the presence of ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 ...
Li J, Xia Z, Ding J (Sep 2005). "Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology ... Nucleic Acids Research. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID 16381901. Ewing RM, Chu P, ... Li J, Xia Z, Ding J (Sep 2005). "Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology ... 13-eicosatetraenoic acid. The amount of expression of adiponectin has been observed to be related to diseases such as insulin ...
"Nucleic Acids Research. 25 (19): 3868-74. doi:10.1093/nar/25.19.3868. PMC 146972 . PMID 9380510.. ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ... RAD51 is involved in the search for homology and strand pairing stages of the process. ... "Nucleic Acids Res. 32 (1): 169-78. doi:10.1093/nar/gkg925. PMC 373258 . PMID 14704354.. ...
"Nucleic Acids Res. 37 (Database issue): D274-8. doi:10.1093/nar/gkn862. PMC 2686586. PMID 19022853.. ... Homology modeling can be used to construct an atomic-resolution model of the "target" integral protein from its amino acid ... sequence and an experimental three-dimensional structure of a related homologous protein. This procedure has been extensively ... is embedded in the hydrophobic regions of the bilayer are alpha helical and composed of predominantly hydrophobic amino acids. ...
Deppenmeier, U. (2002). "The unique biochemistry of methanogenesis". Prog Nucleic Acid Res Mol Biol. Progress in Nucleic Acid ... In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that ... Engelhardt H; Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... "Nucleic Acids Res. 27 (23): 4658-70. doi:10.1093/nar/27.23.4658. PMC 148756 . PMID 10556324.. ...
They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have ... "Nucleic Acids Research. 34 (9): 2653-62. doi:10.1093/nar/gkl338. PMC 1464108. PMID 16714444.. ... compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ...
nucleic acid binding. Cellular component. • intracellular. • cell nucleus. Biological process. • regulation of transcription, ... Chand A, Clark J, Cooper CS, Craig IW (1997). "Long-range organization of reiterated sequences, including the SSX1 cDNA at the ... "Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial ... "The DNA sequence of the human X chromosome". Nature. 434 (7031): 325-37. doi:10.1038/nature03440. PMC 2665286 . PMID 15772651 ...
... nucleic acid - nucleic acid test - nucleocapsid - nucleoli - nucleoside - nucleoside analog - nucleoside reverse transcriptase ... homology (biology) - hormone - host - host factors - HPTN - HPV - HRSA - HTLV-I - HTLV-I-associated myelopathy/tropical spastic ... long terminal repeat sequence (LTR) - long-term nonprogressors - LTR - lumbar - lumbar puncture - lymph - lymph nodes - ... ribonucleic acid (RNA) - ribosome - RNA - route of administration - RT-PCR - RTI - Ryan White C.A.R.E. act ...
"Nucleic Acids Res. 27 (23): 4658-70. PMC 148756. PMID 10556324. doi:10.1093/nar/27.23.4658.. ... Molecular Sequences and the Early History of Life. En: Sapp J, editor. "Microbial Phylogeny and Evolution: Concepts and ... Engelhardt H, Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... "Nucleic Acids Research (39(8)): 3204-3223.. *↑ Christian Rinke; et al. (2013). "Figure 2: Maximum-likelihood phylogenetic ...
... ting transfer may be used for homology-based cloning on the basis of amino acid sequence of the protein product of ... Sequences that hybridize with the hybridization probe are further analysed, for example, to obtain the full length sequence of ... A Southern blot is a method used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern ... If some of the DNA fragments are larger than 15 kb, then prior to blotting, the gel may be treated with an acid, such as dilute ...
Watson, J. D.; Crick, FH (1953). "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" (PDF). Nature ... International Human Genome Sequencing Consortium (October 2004). "Finishing the euchromatic sequence of the human genome". ... Patterson, C (November 1988). "Homology in classical and molecular biology.". Molecular Biology and Evolution 5 (6): 603-25. ... Hershey, AD; Chase, M (1952). "Independent functions of viral protein and nucleic acid in growth of bacteriophage". The Journal ...
"Human lymphotoxin and tumor necrosis factor genes: structure, homology and chromosomal localization". Nucleic Acids Res. 13 ... positive regulation of sequence-specific DNA binding transcription factor activity. • cellular response to nicotine. • positive ... TNF is primarily produced as a 233-amino acid-long type II transmembrane protein arranged in stable homotrimers.[24][25] From ... The sequential and functional homology of TNF and LT led to the renaming of TNF as TNFα (this article) and LT as TNFβ. In 1985 ...
"Nucleic Acids Res. 27 (11): 2291-8. PMC 148793 . PMID 10325416. doi:10.1093/nar/27.11.2291.. ... The SET domain is a 130-amino acid sequence involved in modulating gene activities. This domain has been demonstrated to bind ... "DNA damage, homology-directed repair, and DNA methylation". PLoS Genet. 3 (7): e110. PMC 1913100 . PMID 17616978. doi:10.1371/ ... "Nucleic Acids Research. 40 (22): 11450-62. PMC 3526280 . PMID 23034806. doi:10.1093/nar/gks891.. ...
The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In ... Nucleic Acids Research. 28 (1): 304-05. doi:10.1093/nar/28.1.304. PMC 102465. PMID 10592255. Archived from the original (PDF) ... known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being ... Sequence motif. Short amino acid sequences within proteins often act as recognition sites for other proteins.[26] For instance ...
As N. gonorrhoeae is closely related to N. meningitidis and they have 80-90% homology in their genetic sequences some cross- ... Tests that use polymerase chain reaction (PCR, aka nucleic acid amplification) to identify genes unique to N. gonorrhoeae are ...
"Nucleic Acids Res. 23 (7): 1184-91. doi:10.1093/nar/23.7.1184. PMC 306829 . PMID 7739897.. ... transcription factor activity, sequence-specific DNA binding. • transcription regulatory region DNA binding. • sequence- ... "HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences". J. Biol. Chem. 277 (9): ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. Cellular component. • nucleoplasm. • actin ...
"Nucleic Acids Res. 33 (20): e176. doi:10.1093/nar/gni180. PMC 1292996 . PMID 16314307.. ... length of sequence. {\displaystyle (({\text{number of }}C+{\text{number of }}G)/2)^{2}/{\text{length of sequence}}}. [7]. Many ... "DNA damage, homology-directed repair, and DNA methylation". PLoS Genetics. 3 (7): e110. doi:10.1371/journal.pgen.0030110. PMC ... length of sequence. {\displaystyle ({\text{number of }}C*{\text{number of }}G)/{\text{length of sequence}}}. [6]. or ...
"Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid" (PDF). Nature. 171 (4356): 737-8. Bibcode: ... The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between ... By comparing the homology between different species' genomes, it is possible to calculate the evolutionary distance between ... Next-generation sequencing (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing ...
"Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs". Nucleic Acids Res. 31 (13 ... They discovered that the Pleckstrin Homology domain of AKT binds to PtdIns(3,4,5)P3 (and PtdIns(3,4)P2) and that this binding ... March 1993). "SH2 domains recognize specific phosphopeptide sequences". Cell. 72 (5): 767-78. doi:10.1016/0092-8674(93)90404-E ... August 1997). "A comparative analysis of the phosphoinositide binding specificity of pleckstrin homology domains". J. Biol. ...
Nucleic acids and small molecules are sometimes considered antibody mimetics, but not artificial antibodies, antibody fragments ... Streptococcal IgA1 protease, digestion, Fab and Fc fragments, and the complete amino acid sequence of the alpha 1 heavy chain ... as well as homology models that predict successful docking of antibodies with their unique antigen.[86] ... these scientists deduced the structure and complete amino acid sequence of IgG, a feat for which they were jointly awarded the ...
"Nucleic Acids Research. 15 (16): 6733. doi:10.1093/nar/15.16.6733. PMC 306135 . PMID 2888085.. ... Lüdecke B, Bartholomé K (Jun 1995). "Frequent sequence variant in the human tyrosine hydroxylase gene". Human Genetics. 95 (6 ... Ledley FD, DiLella AG, Kwok SC, Woo SL (Jul 1985). "Homology between phenylalanine and tyrosine hydroxylases reveals common ... amino acid binding. • monooxygenase activity. • protein domain specific binding. Cellular component. • cytoplasm. • cytosol. • ...
... usually amino acids or nucleic acids) is lacking. When grown on media that lacks these nutrients, the yeast fail to survive. ... Determination of sequences crucial for interaction[edit]. By changing specific amino acids by mutating the corresponding DNA ... For a protein with an interacting partner, its functional homology to other proteins may be assessed by supplying the third ... "Nucleic Acids Research. 26 (16): 3700-6. doi:10.1093/nar/26.16.3700. PMC 147751. PMID 9685485.. ...
"Nucleic Acids Res. 26 (3): 847-53. doi:10.1093/nar/26.3.847. PMC 147327. PMID 9443979.. ... When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are ... The double-strand repair mechanism in which BRCA1 participates is homology-directed repair, where the repair proteins copy the ... In their unanimous decision on October 7, 2015 the "high court found that an isolated nucleic acid, coding for a BRCA1 protein ...
Holley and colleagues published the first nucleic acid sequence ever determined, the ribonucleotide sequence of alanine ... including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to ... SequencingEdit. Main article: DNA Sequencing. Historically, sequencing was done in sequencing centers, centralized facilities ( ... Main article: Shotgun sequencing. Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than ...
Nucleic Acids Research. 39 (Web Server issue): W475-8. doi:10.1093/nar/gkr201. PMC 3125724. PMID 21470960.. ... Once a mutation occurs in the DNA or other genetic carrying sequence, there is no way for the mutation to be removed from the ... that catalyses the key functions of DNA homology search and strand exchange in the bacterial sexual process of transformation, ... While DNA is able to recombine to modify alleles, DNA is also susceptible to mutations within the sequence that can affect an ...
"Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" (PDF). Nature (London: Nature Publishing Group ... Shubin, Neil; Tabin, Clifford J.; Carroll, Sean (February 12, 2009). "Deep homology and the origins of evolutionary novelty". ... "Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence". Proc. ... Hall, Brian K. (August 2003). "Descent with modification: the unity underlying homology and homoplasy as seen through an ...
In both GATA1 and GATA1-S, C-ZnF (i.e. C-terminus zinc finger) binds to DNA-specific nucleic acid sequences sites viz., (T/A( ... The amino acids are identified as V=valine; M=methionine; G=glycine; S=serine, D=aspartic acid; Y=tyrosine, R=arginine; W= ... sequence-specific DNA binding. • RNA polymerase II core promoter sequence-specific DNA binding. • DNA binding. • p53 binding. • ... enhancer sequence-specific DNA binding. • RNA polymerase II regulatory region sequence-specific DNA binding. • transcriptional ...
Nucleic Acids Research. 36 (15): 5074-82. doi:10.1093/nar/gkn489. PMID 18663010.. ... TREX1 was called DNase III because it showed sequence homology with dnaQ in E. coli and with eukaryotic DNA polymerase epsilon ... Related sequences[edit]. Sequences have been found in other organisms that encode gene products with a similar function to dnaQ ... Nucleic Acids Research. 41 (10): 5354-67. doi:10.1093/nar/gkt162. PMID 23580545.. ...
"Nucleic Acids Research. 43 (D1): D204-D212. 2014. doi:10.1093/nar/gku989. ISSN 0305-1048. PMC 4384041. PMID 25348405.. ... detectable sequence homology to other proteins of known three-dimensional structure and therefore cannot be modeled by homology ... "Nucleic Acids Research. 45 (D1): D1112-D1116. doi:10.1093/nar/gkw978. PMC 5210655. PMID 27789699.. ... Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding ...
... for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the ... Sequence alignment shows the relations between genes or between proteins, leading to a better understanding of their homology ... be the sequences to be aligned, where n. {\displaystyle n}. and m. {\displaystyle m}. are the lengths of A. {\displaystyle A}. ... being the length of the shorter sequence.. Gap penalty example[edit]. Take the alignment of sequences TACGGGCCCGCTAC. and ...
I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, and J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies Message Subject (Your Name) has sent you a message from PNAS ...
Fri, 21 Oct 2011 , Nucleic Acids There is a high level of sequence homology (98-100%) between D4Z4 repeats from the 4q35 and ... Sequence Homology And Genetic Recombination Between 4q35 And 10q26. ... DNA sequencing was successful in identifying a unique BluI restriction site present only in each copy of the 10q26-derived ... The high degree of homology between the 4q35 and the 10q26 D4F104S1 region is thought to have been responsible for ...
"Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.. ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. ...
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. doi: 10.1093/nar/gkr245. Epub 2011 May 9. Research Support, Non-U.S. ... These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is managed by two members of the ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1BMX Legend Entity #1 , Chains: A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 ...
Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation. ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is managed by two members of the ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1F5X Legend Entity #1 , Chains: A RHO-GEF VAV protein, length: 208 (BLAST ...
... distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence ... Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, ... MIPS: a database for protein sequences, homology data and yeast genome information Nucleic Acids Res. 1997 Jan 1;25(1):28-30. ... homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the ...
... we have cloned and sequenced novel junctions produced by six spontaneous deletion mutations at the aprt locus of Chinese ... To examine the factors governing the generation of DNA sequence rearrangements in mammalian somatic cells, ... Sequence Homology, Nucleic Acid Substances * Pentosyltransferases * Adenine Phosphoribosyltransferase * DNA Restriction Enzymes ... Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad ...
Modelling of proteins and nucleic acids. • Sequence alignments and sequence homology. • Homology modelling. • De novo modelling ... Key elements of biochemistry: proteins, peptides, nucleic acids, lipids, and small molecules. • Important metabolic pathways. ... This will include structure prediction using homology and ab initio protein modelling, building protein-ligand and protein- ...
"Homology" in proteins and nucleic acids: A terminology muddle and a way out of it". Cell. 50 (5): 667. doi:10.1016/0092-8674(87 ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Homologous sequence regions are also called conserved. This is not to be confused with conservation in amino acid sequences, ... Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. The term "percent homology ...
The primary amino acid sequence of the toxin was deduced from the nucleotide sequence data. entC3 contains 801 bp and encodes a ... which encodes staphylococcal enterotoxin C3 was cloned from the genome of Staphylococcus aureus FRI-913 and sequenced. ... Molecular Sequence Data * Molecular Weight * Protein Precursors / genetics * Sequence Homology, Nucleic Acid ... The primary amino acid sequence of the toxin was deduced from the nucleotide sequence data. entC3 contains 801 bp and encodes a ...
Sequence Homology, Nucleic Acid • Serine • Serotonin • Serotonin Plasma Membrane Transport Proteins • Serotonin Receptor ... Folic Acid • Folic Acid Deficiency • Food • Food Deprivation • Formate-Tetrahydrofolate Ligase • Gene Expression • Gene ... Abdomen • Abscisic Acid • Acetaminophen • Acetylcholinesterase • Actins • Action Potentials • Adaptation, Biological • ... Pyrrolidonecarboxylic Acid • Quantitative Trait Loci • Quantitative Trait, Heritable • Raphe Nuclei • Rats • Receptor, Insulin ...
Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has ... epigenome and genome sequence variation data. Nucleic Acids Res. 2015;43(Database issue):D87-91.View ArticleGoogle Scholar. ... Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis. *Natalia Polouliakh1, 2, 3Email author ... Nucleic Acids Res. 2009;37(Web Server issue):W202-8.View ArticleGoogle Scholar. ...
Sequence Homology, Nucleic Acid. *DUX4. *p53 Protein. *MDM2. *Cancer Gene Expression Regulation ... Using a luciferase reporting system and sequence analysis, the potential target of miR-411-5p was identified as sprouty homolog ... Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel the ... Given that the Pax3-Foxo1 fusion gene will contain all the regulatory sequences necessary for precise regulation of its ...
... was isolated and its DNA sequence determined. The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence ... A cDNA clone encoding the complete coding sequence for porcine alpha-1-antitrypsin (or alpha 1-protease inhibitor, PI) ... Sequence Analysis, DNA. Sequence Homology, Amino Acid. Sequence Homology, Nucleic Acid. Swine / genetics*. alpha 1-Antitrypsin ... was isolated and its DNA sequence determined. The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence ...
Molecular Sequence Data. *RNA. *Sequence Homology, Nucleic Acid. *Peptide Fragments. *Biomarkers, Tumor ... Multiplexed amplicon sequencing of PCR products from bisulfite-treated DNA of matched CRC and non-neoplastic tissue as well as ... Because there is no data available about the transcription factors which bind to ING1 promoter, the promoter sequence was ... qMSP assays were developed for 32 genes, including 15 of the sequenced genes, and used to quantify methylation in tumor, ...
Nucleic Acid Hybridization. Oncogenes*. RNA. Sequence Homology, Nucleic Acid. Transcription, Genetic. Trophoblasts / physiology ... 18639569 - Gene expression profiles modulated by the human carcinogen aristolochic acid i in human.... 7903339 - Molecular ...
Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 - 1st Edition. Print Book & E-Book. ISBN 9780121820848, ... C.B. Lawrence, Use of Homology Domains in Sequence Similarity Detection.. M. Gribskov, R. L~aduthy, and D. Eisenberg, Profile ... J.C.W. Shepherd, Ancient Patterns in Nucleic Acid Sequences.. R. Staden, Searching for Patterns in Protein and Nucleic Acid ... Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 1st Edition. 0.0 star rating Write a ...
... sequences identified in a wide variety of organisms ... Homology search with fragmented nucleic acid sequence patterns ... Nucleic Acids Res. 36:W5‐W9. doi: 10.1093/nar/gkn201.. Jossinet, F. and Westhof, E. 2005. Sequence to Structure (S2S): Display ... Nucleic Acids Res. 42:D764‐D770. doi: 10.1093/nar/gkt1168.. Katoh, K. and Standley, D.M. 2013. MAFFT multiple sequence ... Web servers for analyses of RNA sequences. Nucleic Acids Res. 36:W75‐W78. doi: 10.1093/nar/gkn222. ...
PF4 promoter sequences. The sequences have been aligned in a manner to maximize their homology. The nucleic acid sequence ... refers to a nucleic acid sequence that regulates the transcription of its corresponding nucleic acid coding sequence or ... 2 depicts the nucleic acid sequence of a Sprague-Dawley rat PF4 promoter as originally sequenced(SEQ ID NO:1). ... Depending upon the nucleic acid sequence(s) inserted and the level of expression in the mammal, the mammal may become more or ...
Sequence homology between human and animal rotavirus serotype-specific glycoproteins. Nucleic Acids Res. 1984;12:3937-82. DOI ... The VP7 genes had nucleotide and amino acid homology of ,99% identity. Alignment of the deduced amino acid sequences of the VP7 ... nucleotide identity and amino acid homology with the nonoutbreak strains. Alignment of the deduced amino acid sequences showed ... Sequence Analysis. Figure 3. Figure 3. Deduced amino acid sequences of the VP7 antigenic regions of rotavirus G9P[8] strains. A ...
1997) MIPS: A database for protein sequences, homology data and yeast genome information. Nucleic Acids Res 25(1):28-30. ... 2004) SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res 32(Database issue): ... All the sequences within a Pfam family with structural information available are aligned to sequences of the PDB crystal ... The rationale is that the positions determine the separation of the sequences and, at the same time, the sequence separation ...
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W526-31. doi: 10.1093/nar/gkp316. Epub 2009 May 6. ... HorA web server to infer homology between proteins using sequence and structural similarity. ... Nucleic Acids Res. 2009 Jul;37(Web Server issue):W532-8. doi: 10.1093/nar/gkp328. Epub 2009 May 5. ... Nucleic Acids Res. 2012 Jul;40(12):5189-200. doi: 10.1093/nar/gks226. Epub 2012 Mar 9. Review. ...
Repetitive Sequences, Nucleic Acid. *Retrotransposons*. *Sequence Homology, Amino Acid. *Support, Non-U.S. Govt ... A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse ... these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The ... DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that ...
The invention relates to the protein and nucleic acids encoding the protein. The invention further relates to an assay system ... The nucleic acid sequence of EER-7 shows homology to known lysyl oxidase genes. All previously identified lysyl oxidase ... The present invention provides a novel LO protein termed EER-7. Nucleic acid sequences, protein sequence, nucleic acid and ... the isolated nucleic acid lacks one or more introns. Isolated nucleic acid molecules include sequences inserted into plasmids, ...
... probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. *^ Söding J (2005). "Protein homology ... sequences of S. {\displaystyle S}. until the modified sequences, S. i. ′. {\displaystyle S_{i}^{}}. , all conform to length L ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences ...
Molecular Sequence Data Restriction Mapping Sequence Homology, Nucleic Acid Vitelline Membrane Substances DNA, Complementary ... Amino Acid Sequence Animals Base Sequence Cloning, Molecular DNA, Complementary Drosophila Proteins Drosophila melanogaster Egg ... Sequence analysis of genomic and cDNA clones for the two genes, VM26A.1 and VM34C.1, indicates that both are similarly ... Comparative analysis of the sequence and structure of two Drosophila melanogaster genes encoding vitelline membrane proteins. L ...
For example, the amino acid sequence of the E. coli RpoD is very well preserved among a very large number of Gram− bacteria ( ... 1992). "Stable Propagation of Cosmid Sized Human DNA Inserts in an F-Factor Based Vector." Nucleic Acids Research 20(5): 1083- ... KEGG database Eco RpoD (2010). "Protein sequence homology search for E. coli k12 R p o D protein." ... 1991). Amplified 16S RNA genes will be cloned (in pCR®8/GW/TOPO) for sequencing to compare them with the nonredundant sequence ...
  • Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (
  • These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. (
  • Multiple sequences alignments (MSAs) provide essential information on the evolution of protein families. (
  • 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. (
  • 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. (
  • Therefore it make sense to construct an algorithm to assist in repetitive calculations of multiple sequence alignments. (
  • A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (
  • CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. (
  • 227] Pritha Ghosh, Teerna Bhattacharya, Oommen K. Mathew and R. Sowdhamini (2019) PASS2 version 6 a database of structure based sequence alignments of protein domain superfamilies in accordance with SCOPe. (
  • S4: structure-based sequence alignments of SCOP superfamilies. (
  • Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. (
  • Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5′-triphosphatase domain. (
  • In this study, we used sequence- and structure-based alignments with related proteins to predict the structure of VP3 and identify enzymatic domains and active sites therein. (
  • In the absence of an affordable and capable technology to generate and assemble a conifer genome, previous investigations have relied on other techniques to generate sequence for basic and applied research in pine genetics. (
  • Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. (
  • Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (
  • The term "percent homology" is often used to mean "sequence similarity. (
  • The percentage of identical residues ( percent identity ) or the percentage of residues conserved with similar physicochemical properties ( percent similarity ), e.g. leucine and isoleucine , is usually used to "quantify the homology. (
  • Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (
  • As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution , or, as with shorter sequences, by chance, meaning that they are not homologous. (
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, [4] inherited from the shared ancestor . (
  • i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. (
  • The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence similarity to the corresponding cDNAs for human, baboon, rat, mouse, sheep and cow. (
  • C.B. Lawrence , Use of Homology Domains in Sequence Similarity Detection. (
  • HorA web server to infer homology between proteins using sequence and structural similarity. (
  • 1. An isolated nucleic acid encoding an endothelial estrogen regulated gene-7 protein that has (i) an amino acid sequence which has at least about 95% sequence similarity with SEQ ID NO: 2 and (ii) lysyl oxidase activity. (
  • Homologous proteins (proteins who have common ancestry) are inferred from their sequence similarity. (
  • A FIGURE NEEDS TO GO HERE THIS IS THE CAPTION) "Sequence search/alignment algorithms find the path that maximizes the sum of similarity scores (color-coded blue to red). (
  • Cytosine methyltransferases can also be categorized on the basis of enzyme structure and similarity of conserved amino acid motifs. (
  • Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may represent homologies. (
  • Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. (
  • Homology -- Similarity of nucleotide or amino acid sequences in nucleic acids, peptides, or proteins. (
  • The deduced amino acid sequence of APO-1 showed sequence identity with the Fas antigen, a cysteine-rich transmembrane protein of 335 amino acids with significant similarity to the members of the tumor necrosis factor/nerve growth factor receptor superfamily. (
  • Bet v 1 has been identified as existing in three subfamilies, based on the sequence similarity. (
  • 1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. (
  • PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. (
  • Through its WWW server ( ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (
  • A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. (
  • The structural gene entC3, which encodes staphylococcal enterotoxin C3 was cloned from the genome of Staphylococcus aureus FRI-913 and sequenced. (
  • One sequence, Ta17, is located in the mitochondrial genome. (
  • The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families. (
  • In addition, flat file access to the FASTA sequences of the genome and transcriptome, annotations, and gff3 files are available through the database FTP site ( ). (
  • In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine ( Pinus taeda L.), which comprises 20.1 Gb of sequence. (
  • To date, the only complete bacterial genome sequences lacking candidate RM systems are from the obligate intracellular parasites Chlamydia and Rickettsia . (
  • Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (
  • With the advent of the post genome era and the development of sequencing technology, how to find all forms of miRNAs from millions of reads has become one of the challenging topics in bioinformatics. (
  • Many eukaryotes preferentially use the NHEJ pathway to repair a DSB, and exogenous targeting DNA can be integrated anywhere into the genome independent of DNA sequence homology ( 27 ). (
  • of these 44, 10 are homologous to entries in the complete K-12 genome sequence, 4 are nearly identical to the sequences of E. coli J96 encoding the HlyA hemolysin, 11 encode P fimbriae, and 19 show no homology to J96 or K-12 entries. (
  • 30-kb) blocks of DNA inserted within or near tRNA genes ( 12 , 33 , 39 ), contain direct repeats and insertion sequences, have a GC content that differs from that of the rest of the genome, and encode defined virulence determinants ( 3 , 19 , 26 ). (
  • Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. (
  • Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. (
  • DNA, or deoxyribonucleic acid -- The primary genetic material of all cellular organisms and the DNA viruses. (
  • RNA, viral -- Ribonucleic acid that makes up the genetic material of viruses. (
  • Several lines of experimental evidence argue in favor of a dominant role of positive selection for amino acid changes in driving the pattern of HVR1 genetic diversification ( 1 , 2 ). (
  • citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (
  • The serotype has been identified since 1996 as a frequent nucleotide sequences in genes encoding three rotavirus cause of severe disease in hospitalized children from many proteins, VP7, VP8, and NSP4, but they were distinct from countries, including the United States, Japan, India, G9P[8] strains isolated in previous years. (
  • Sequence comparison of mitochondrial tRNA genes and origin of light strand replication in Bos taurus. (
  • The outbreak strains showed identical nucleotide sequences in genes encoding three rotavirus proteins, VP7, VP8, and NSP4, but they were distinct from G9P[8] strains isolated in previous years. (
  • Comparative analysis of the sequence and structure of two Drosophila melanogaster genes encoding vitelline membrane proteins. (
  • 2000 ) identified maize ( Zmet3 ) and Arabidopsis ( DRM ) genes encoding proteins closely related to Dnmt3 methyltransferases but containing a novel arrangement of the eight diagnostic methyltransferase amino acid motifs. (
  • Such genes significantly affected the metabolism of lipid, cellular ketone, organic acid, and carboxylic acids. (
  • Compilation of tRNA sequences and sequences of tRNA genes. (
  • Consensus sequences noted in many other eukaryotic genes, as well as histone-specific consensus sequences, have been identified. (
  • An unusual feature of the spacer region between the H4 and H2B genes is the presence of a duplicated sequence 87 bp in length. (
  • Connor W, States JC, Mezquita J, Dixon GH (1984b) Organization and nucleotide sequence of rainbow trout histone H2A and H3 genes. (
  • Antisense peptide nucleic acids (PNAs) exhibit growth inhibitory effects on bacteria by inhibiting the expression of essential genes and could be promising therapeutic agents for treating bacterial infections. (
  • The 57,988-bp stretch of DNA has characteristics which define PAIs, including a size greater than 30 kb, the presence of insertion sequences, distinct segmentation of K-12 and J96 origin, GC content (42.9%) different from that of total genomic DNA (50.8%), and the presence of virulence genes ( hly and pap ). (
  • Nucleotide sequence analysis of the chorea mAb V H genes revealed that mAb 24.3.1 V H gene was encoded by the V H 1 germline gene family which encodes other anti-ganglioside V H genes associated with motor neuropathies. (
  • Endoproteinase-cleaved peptides of the APO-1 protein were subjected to amino acid sequencing, and corresponding oligonucleotides were used to identify a full-length APO-1 cDNA clone from an SKW6.4 cDNA library. (
  • Peptides containing this sequence motif exhibited monocyte activating capacity similar to the autocrine stimulatory capacity of hTNF alpha itself. (
  • A high number of specific clones was obtained after immunization with a pool of nine mimotopes, and the resulting mAbs were shown to recognize several 16- and 27-mer peptides derived from natural HVR1 sequences isolated from patients with acute and chronic HCV infection, suggesting that HVR1 mimotopes were efficient antigenic and immunogenic mimics of naturally occurring HCV variants. (
  • Prospective studies of serological responses to synthetic oligopeptides derived from HVR1 sequences of patients with acute and chronic HCV infection showed apparently extensive serological cross-reactivity for unrelated HVR1 peptides in the majority of the patients ( 3 , 4 , 5 , 6 , 7 , 8 , 9 ). (
  • 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. (
  • CS-BLAST (Context-Specific BLAST) is a tool that searches a protein sequence that extends BLAST (Basic Local Alignment Search Tool), using context-specific mutation probabilities. (
  • It was possible to use this CRISPR system to create a single conserved amino acid substitution (A189G) mutation for both alleles of RAD51 , a DNA recombinase involved in homology-directed repair. (
  • These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. (
  • H.M. Martinez , Detecting Pseudoknots and Other Local Base-Pairing Structures in RNA Sequences. (
  • Notwithstanding, the information currently available on protein sequences, structures, functions, and interactions opens the door to performing more comprehensive studies of the relationships between family organization and functional divergence ( 17 ). (
  • Multiple sequence alignment is often used to assess sequence conservation of protein domains , tertiary and secondary structures, and even individual amino acids or nucleotides. (
  • Homology is the relationship between biological structures or sequences derived from a common ancestor. (
  • of fast alignment algorithms construct auxiliary data structures, called indices, for the read sequences or the reference sequence, or sometimes both. (
  • MARs are typically AT-rich elements that contain consensus cleavage sites for topoisomerase II, and they may contain one or more loosely defined short sequence motifs, but, in general, their structures are not highly homologous. (
  • The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the sequences and secondary structures, which are capable of characterizing the sequence evolution information and sequence-order information, and global and local information of pre-microRNAs secondary structures. (
  • On the other hand, as mature miRNAs are very short, the traditional feature engineering approaches [ 4 ] are usually failed to extract effective features from their sequences and structures. (
  • The search process is a typical alignment problem of sequences and structures. (
  • PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. (
  • Once confined only to experts in bioinformatics, protein sequence retrieving, aligning and modeling tasks are now being routinely approached by an increasing number of researchers, who can take also advantage of the growing number of structures that are being deposited every day in public databases. (
  • A sequence alignment of mammalian histone proteins. (
  • T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. (
  • This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. (
  • The top part is a color-coded alignment where sequences in red correspond to alignment portions with a strong support in the primary library. (
  • M.S. Waterman and R. Jones , Consensus Methods for DNA and Protein Sequence Alignment. (
  • D.-F. Feng and R.F. Doolittle , Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences. (
  • G.J. Barton , Protein Multiple Sequence Alignment and Flexible Pattern Matching. (
  • G.M. Landau, U. Vishkin, and R. Nussinov , Fast Alignment of DNA and Protein Sequences. (
  • Accurate multiple sequence‐structure alignment of RNA sequences using combinatorial optimization. (
  • First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. (
  • A multiple sequence alignment ( MSA ) is a sequence alignment of three or more biological sequences , generally protein , DNA , or RNA . (
  • Multiple sequence alignment also refers to the process of aligning such a sequence set. (
  • 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. (
  • 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. (
  • The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. (
  • A DIFFERENT GRAPH NEEDS TO GO HERE) CS-BLAST offers improved sensitivity and alignment quality in sequence comparison. (
  • This page shows the publications Kiran Musunuru has written about Sequence Alignment. (
  • A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. (
  • We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing. (
  • The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. (
  • Each tool must be considered as standalone (e.g., it's possible to perform a sequence alignment task without searching in the database as a mandatory step). (
  • PyMod has a rich functionality, based on its core sequence alignment, clustering and editing window. (
  • The protein sequence alignment was performed by T-Coffee method. (
  • In the current study, we used sequence alignment and homology modeling to identify features common to nonturreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. (
  • Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. (
  • DDBJ in collaboration with mass-sequencing teams on annotation. (
  • geneid - Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. (
  • Determination and augmentation of RNA sequence specificity of the Nova K-homology domains. (
  • Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (
  • This involves that the term "percent homology" is a misnomer. (
  • Sequences are the middle 120-180 amino acid residues of the proteins. (
  • Residues that are conserved across all sequences are highlighted in grey. (
  • The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both and its main mirror (
  • Thus, the first 27 residues of the toxin precursor comprise the signal peptide, and the mature toxin contains 239 amino acids with a molecular weight of 27,563 daltons. (
  • Enterotoxin C3 differs from enterotoxin C2 by four amino acids and from enterotoxin C1 by nine residues. (
  • The 167 C-terminal residues of the three toxins are identical, except for one conservative amino acid substitution in enterotoxin C3. (
  • 1985) determined that human plasma Hx consists of a single polypeptide chain of 439 amino acids residues with six intrachain disulfide bridges and has a molecular mass of approximately 63 kD. (
  • The complete sequence of a beta-mannanase gene from an anaerobic extreme thermophile was determined, and it shows that the expressed protein consists of two catalytic domains and two binding domains separated by spacer regions rich in proline and threonine residues. (
  • The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is a highly heterogeneous sequence that is promiscuously recognized by human sera via binding to amino acid residues with conserved physicochemical properties. (
  • The positions in MSAs can be interpreted in terms of the amino acid changes allowed or disallowed during evolution, and therefore useful information at the residue level can be inferred from them ( 4 ). (
  • Her research focuses on developing hydrogel-based platforms and biosensors for the detection and sensing of circulating nucleic acid biomarkers from liquid biopsy. (
  • Antisense/antigene therapy using peptide nucleic acids (PNAs) has the potential to help control MDR bacterial infections. (
  • The high degree of homology between the 4q35 and the 10q26 D4F104S1 region is thought to have been responsible for interchromosomal exchanges between these two regions. (
  • Homologous sequence regions are also called conserved . (
  • R. Staden , Finding Protein Coding Regions in Genomic Sequences. (
  • Several of the amino acid substitutions on the VP7 and NSP4 proteins were identified in regions known to influence function and may have contributed to the emergence and increased dominance of the outbreak strains. (
  • UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. (
  • Here, the bioinformatic algorithms were applied for known Bet v 1 homologous nucleic acids sequences to find homology and conserved regions. (
  • Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. (
  • These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods. (
  • Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. (
  • From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (
  • Universal phylogenetic tree based on the 16S rRNA gene sequence comparisons. (
  • A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. (
  • 4. A chimeric gene capable of transforming a plant cell of an oil-producing species comprising a nucleic acid fragment of Claim 1 operably linked to suitable regulatory sequences resulting in overexpression of said soybean seed stearoyl-ACP desaturase in the plastid of said plant cell. (
  • These methods mainly utilize the conservation characteristics of miRNAs and their precursor sequences in multiple species to search for the conserved sequences in the intergenic region. (
  • Genomic sequences of PR proteins of two different fruit species, which allergens belong to PR proteins of the same type as Bet v 1, were selected to design degenerate primers. (
  • Subsequently, screening of the presence of Bet v 1 conserved genomic sequence was performed in 45 clinically relevant plant species. (
  • Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2′- O -methyltransferase domain for most rotavirus species. (
  • PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. (
  • We have developed methodologies for the molecular identification of rotavirus strains based on VP7 gene segment sequence. (
  • The protein sequence of H4, as determined from the nucleic acid sequence, is the same as that derived for other vertebrate H4 proteins, although comparison of nucleotide sequences shows a great deal of sequence divergence, especially in the third base position. (
  • However, these methods can only find highly homologous miRNAs with known miRNA sequences and require a large amount of computational resource for whole genomes. (
  • The homologous recombination pathways repair a DSB using mechanisms that recognize highly homologous DNA sequences, while the nonhomologous end-joining (NHEJ) pathway does not rely on DNA sequence homology. (
  • VT1 is highly homologous to Stx of Shigella dysenteriae type I. VT2 shares approximately 55% amino acid homology with VT1 but is relatively more heterogeneous. (
  • This is not to be confused with conservation in amino acid sequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties. (
  • Smyth, V.A., Higgins, D.G., and Kennedy, B.N. (2011) mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation. (
  • DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. (
  • 2010). "A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridiu/I7 acetobutylicu/I7 involving non-coding RNAs and ribosomal RNA processing. (
  • Centromeric repeat arrays hypomethylated in met1-1 mutants are partially remethylated when introduced into a wild-type background, in contrast to genomic sequences hypomethylated in ddm1 mutants. (
  • The complete nucleotide sequence of the 3.0-kb BamH I-Sst I restriction fragment contained within the rainbow trout genomic clone λTH2 has been determined. (
  • To determine whether sequences found within the junctions of the PAI of CFT073 were common to other uropathogenic strains of E. coli , 11 probes were isolated along the length of the PAI and were hybridized to dot blots of genomic DNA isolated from clinical isolates (67 from patients with acute pyelonephritis, 38 from patients with cystitis, 49 from patients with catheter-associated bacteriuria, and 27 from fecal samples). (
  • Computer analysis of the uvrD coding sequence has indicated that it contains seven conserved motifs that are shared by a superfamily of proteins involved in DNA metabolism ( 16 ). (
  • Motifs IA, IB, and II, previously identified as Walker A and Walker B sequences, respectively, are conserved segments found in many nucleoside triphosphate-binding proteins and all helicases characterized to date ( 14 , 15 , 46 ). (
  • Combining expression and sequence data: searching for motifs in expression clusters (Tavazoie), linear contribution of motifs to expression levels (Bussemaker), combinations of motifs (Pilpel). (
  • MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. (
  • W.C. Barker, D.G. George, and L.T. Hunt , Protein Sequence Database. (
  • J.F. Collins and A.F.W. Coulson , Significance of Protein Sequence Similarities. (
  • Protein sequence homology search for B. subtilis RpoD. (
  • Protein sequence design and its applications. (
  • STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. (
  • In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. (
  • Integrating protein sequence and structure information has therefore become an imperative, especially in the field of protein structure prediction from sequence, by means of homology modeling (HM) methodologies. (
  • In recent years, a number of valuable tools related to protein sequence analysis and modeling (e.g. (
  • A cDNA clone encoding the complete coding sequence for porcine alpha-1-antitrypsin (or alpha 1-protease inhibitor, PI) was isolated and its DNA sequence determined. (
  • 4. The isolated nucleic acid of claim 1 , which is a cDNA. (
  • 6. The isolated nucleic acid of claim 5 , which is a cDNA. (
  • 8. The isolated nucleic acid of claim 7 , which is a cDNA. (
  • The complete cDNA sequence and expression of the first major allergenic protein of Malassezia furfur , Mal f 1," European Journal of Biochemistry , vol. 246, no. 1, pp. 181-185, 1997. (
  • DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. (
  • In addition, computer-assisted analysis revealed a potential ATP -binding domain in the predicted UL37 amino acid sequence. (
  • Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA-RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3. (
  • Sequence analysis demonstrated 100% homology with a rabies virus variant associated with the silver-haired bat ( Lasionycteris noctivagans ). (
  • 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. (
  • Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. (
  • The goal of this review is to describe not only the mechanism and limits of bacterial 16S rRNA gene sequence analysis but also the impact and potential contribution that the 16S rRNA gene sequence analysis can make to the understanding of clinical microbiology and infectious diseases. (
  • Computer-assisted analysis of the internal homology in amino acid sequence suggested duplication of an ancestral gene thus indicating that Hx consists of two similar halves. (
  • In this report, we provide an analysis of the nucleotide sequence for a 57,988-bp region. (
  • Further examination of samples typed by these methods, such as by sequence analysis, is usually required to further characterize diversity within serotypes. (
  • PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. (
  • In order to contribute to tackle these issues, a simple and intuitive interface between the open-source and widely used biomolecular visualization program PyMOL [ 6 ] and several other well-known sequence/structure analysis tools (i.e. (
  • The tool presented here, PyMod, aims to give researchers and students with no or a limited familiarity in this field, as well as more experienced users, the ability to exploit popular algorithms in sequence/structure analysis and protein structure prediction, and most importantly full customization and control over their parameters, while retaining as much as possible an ease of use and the familiarity of the PyMOL environment (Figure 1 ). (
  • Bioinformatic analysis predicts a target binding sequence for miR-144 at the 32-UTR of meis1 . (
  • Two organisms that are very closely related are likely to display very similar DNA sequences between two orthologs. (
  • Due to the rapid development of "-omics" technology, such as DNA microarrays [ 1 ] and next-generation sequencing (NGS) [ 2 , 3 ], scientists are now able to quantify large numbers of transcripts from organisms simultaneously. (
  • 1. A vector comprising a nucleic acid molecule encoding the SV40 early region tsA58 mutant operably linked to a rat PF4 promoter. (
  • The DNA construct comprises a mammalian metallothionein gene promoter sequence fused to the mammalian hormone sequence of interest. (
  • However, most of them mainly focus on secondary structure information of pre-microRNAs, while ignoring sequence-order information and sequence evolution information. (
  • We use new features for the machine learning algorithms to improve the classification performance by characterizing both sequence order evolution information and secondary structure graphs. (
  • These sequences have a better secondary structure of stem ring. (
  • 1. An isolated nucleic acid fragment comprising a nucleotide sequence encoding the soybean seed stearoyl-ACP desaturase corresponding to the nucleotides 70 to 1245 in SEQ ID NO: 1, or any soybean nucleic acid fragment substantially homologous therewith encoding a functional stearoyl-ACP desaturase with the exception of a nucleic acid fragment having the sequence disclosed in Figure 2 of WO 91/13972. (
  • HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. (
  • The structure of protein families is shaped by the sequence divergence accumulated as a consequence of speciation, gene duplication, and deletion events, as well as by the evolutionary selective pressure exerted on each protein in accordance with the corresponding 3D structure and the specific function performed ( 1 , 2 ). (
  • 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. (
  • Clerc RG, Bucher P, Strub K, Birnstiel ML (1983) Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the −50 region. (
  • 1991 ) Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. (
  • 1991 ) Nuclear targeting sequences- a consensus? (
  • 22. An isolated oligonucleotide primer or probe of 50-100 nucleotides, wherein said oligonucleotide comprises at least 20 consecutive nucleotides of SEQ ID NO: 1 and hybridizes under highly stringent conditions of 0.2 SSC at 68 C. and a washing condition of 50% formamide, 4 SSC at 42 C. with a nucleic acid having the nucleotide sequence of SEQ ID NO: 1. (
  • In order to have a homologous relationship, the sum of scores over all the aligned pairs of amino acids or nucleotides must be sufficiently high [2]. (
  • Similarities between amino acids or nucleotides are quantified in these substitution matrices. (
  • Anticodon -- A sequence of three adjacent nucleotides in tRNA that binds to a complementary codon in mRNA and designates a specific amino acid during protein synthesis. (
  • Codon -- A sequence of three RNA or DNA nucleotides that specifies, i.e., codes for, either an amino acid or the termination of translation. (
  • Such hybridization is highly specific and, therefore, enables identification of different types and sequences of DNA and RNA. (
  • To examine the factors governing the generation of DNA sequence rearrangements in mammalian somatic cells, we have cloned and sequenced novel junctions produced by six spontaneous deletion mutations at the aprt locus of Chinese hamster ovary cells. (
  • The 5′ and 3′ ends of each repeat are complementary, and each repeat contains smaller repeated sequences internally, as well as a possible cruciform structure. (
  • Cloning and sequencing of cDNAs corresponding to mite major allergen Der fll. (
  • Abstract Rapidly evolving sequencing technologies produce data on an unparalleled scale. (
  • Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (
  • T. Gojobori, E.N. Moriyama, and M. Kimura , Statistical Methods for Estimating Sequence Divergence. (
  • Production of transgenic mammals involves the insertion of novel nucleic acid sequences into one or more chromosomes of the mammal. (
  • In vertebrate cells, the elimination of DSBs with minimal nucleotide sequence change involves the spatiotemporal orchestration of an apparently endless number of proteins ranging, according to their action, from the nucleotide level to nucleosome organization and chromosome architecture. (
  • W.R. Taylor , Hierarchical Method to Align Large Numbers of Biological Sequences. (
  • This will include structure prediction using homology and ab initio protein modelling, building protein-ligand and protein-protein complexes and fitting the atomistic data to lower-resolution sets. (
  • The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. (
  • This is calculated with the fraction: (pairs correctly aligned)/(pairs aligned) The graph is the benchmark Biegert and Söding used to evaluate homology detection. (
  • NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (
  • however, their naturally low abundance, short length and high sequence homology represent a major challenge for quantitative and specific detection. (
  • Synthetic insertion signal sequences enhance MHC class I presentation of a peptide from the melanoma antigen MART-1, 2000, Eur. (
  • A nested, reverse transcription polymerase chain reaction assay performed on saliva samples was positive for evidence of rabies virus nucleic acid. (
  • There is a high level of sequence homology (98-100%) between D4Z4 repeats from the 4q35 and the 10q26 D4F104S1 loci. (
  • DNA sequencing was successful in identifying a unique BluI restriction site present only in each copy of the 10q26-derived repeat units[10] and a XapI site in all 4q35-derived repeats. (
  • Our analyses indicate that these rearrangements were produced by non-homologous recombinational events occurring between short (2-7 bp) sequence repeats at the two termini of the deletion which leave one copy of the repeat in the mutant gene. (