Sequence homology nucleic acid. Medical search

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 3.4.21.4.

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 2.7.7.49.

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)

August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi: ... 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 ...

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

"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 ...

https://en.wikipedia.org/wiki/CS-BLAST

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). " ...

https://en.wikipedia.org/wiki/DDX5

"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 ...

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

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 ...

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

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- ...

https://en.wikipedia.org/wiki/Bioinformatics_discovery_of_non-coding_RNAs

"Nucleotide sequence of transforming human c-sis cDNA clones with homology to platelet-derived growth factor". Nucleic Acids Res ...

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

"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 ...

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

... 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". ...

https://en.wikipedia.org/wiki/ORM1

... "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 ...

https://en.wikipedia.org/wiki/RAP2B

This unstructured stretch of sequence may be exposed to allow for interactions with nucleic acids or other proteins. The sisRNA ... sequence is ~100% conserved in EBV strains and homology extends to include other lymphocryptoviruses. The hairpin structure is ... Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform ... Epstein-Barr virus stable intronic-sequence RNAs (ebv-sisRNAs) are a class of non-coding RNAs generated by repeat introns in ...

https://en.wikipedia.org/wiki/Epstein–Barr_virus_stable_intronic-sequence_RNAs

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 ...

https://en.wikipedia.org/wiki/Cadang-cadang

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". ...

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

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. ...

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

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, ISBN 0-521-62971 ...

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

... 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 ...

https://en.wikipedia.org/wiki/T-Coffee

... 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 ...

https://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites:_Bsa–Bso

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- ...

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

... complete coding sequence and homology with other type II topoisomerases". Biochimica et Biophysica Acta (BBA) - Gene Structure ... Nucleic Acids Research. 21 (16): 3719-3723. doi:10.1093/nar/21.16.3719. PMC 309874. PMID 8396237. Nakano H, Yamazaki T, ... Activation of more than 600 regulatory sequences in promoters and 800 regulatory sequences in enhancers, in many cell types, ... Nucleic Acids Research. 20 (21): 5587-5592. doi:10.1093/nar/20.21.5587. PMC 334390. PMID 1333583. "Entrez Gene: TOP2B ...

https://en.wikipedia.org/wiki/TOP2B

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 ...

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

... probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. Söding J (2005). "Protein homology ... Notredame C, Higgins DG (April 1996). "SAGA: sequence alignment by genetic algorithm". Nucleic Acids Res. 24 (8): 1515-24. doi: ... Notredame C, O'Brien EA, Higgins DG (1997). "RAGA: RNA sequence alignment by genetic algorithm". Nucleic Acids Res. 25 (22): ... Edgar RC (2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): ...

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

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 ...

https://en.wikipedia.org/wiki/RNASE1

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. ...

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

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 ...

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

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 ...

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

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 ...

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

... 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 ...

https://en.wikipedia.org/wiki/List_of_MeSH_codes_(G13)

... nucleic acid sequence - synapomorphy - homology - molecular clock - outgroup (cladistics) - maximum parsimony (phylogenetics ... genetic map DNA Nucleic acid double helix Nucleobase: adenine (A) - cytosine (C) - guanine (G) - thymine (T) - uracil (U) DNA ... phospholipids nucleic acids: DNA - RNA Outline of cell biology Cell structure: Cell coined by Robert Hooke Techniques: cell ... sequencing - shotgun sequencing - cloning - culture - DNA microarray - electrophoresis - protein tag - affinity chromatography ...

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

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 ...

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

"The HSSP database of protein structure-sequence alignments". Nucleic Acids Research. 25 (1): 226-230. doi:10.1093/nar/25.1.226 ... HSSP (Homology-derived Secondary Structure of Proteins) is a database that combines structural and sequence information about ... HSSP is also a database of homology-based implied protein structures. Protein Data Bank (PDB) STING Schneider, R.; de Daruvar, ...

https://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins

Nucleic Acids Research. 41 (Database issue): D536-44. doi:10.1093/nar/gks1080. PMC 3531119. PMID 23161684. Stein, L. (2001). " ... Once a genome is sequenced, it needs to be annotated to make sense of it. Genes in a eukaryotic genome can be annotated using ... A simple method of gene annotation relies on homology based search tools, like BLAST, to search for homologous genes in ... Genome annotation remains a major challenge for scientists investigating the human genome, now that the genome sequences of ...

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

The standard methods of testing for presence of SARS-CoV-2 are nucleic acid tests, which detects the presence of viral RNA ... homology with pangolin SARS-CoV, and has 90% homology with the M protein of SARS-CoV; whereas, the similarity is only around 38 ... In January 2020, the SARS-CoV-2 genetic sequence data was shared through GISAID, and by March 2020, the global pharmaceutical ... COVID-19 testing methods to detect the virus's nucleic acid include real-time reverse transcription polymerase chain reaction ( ...

https://en.wikipedia.org/wiki/COVID-19

... all-atom contacts and structure validation for proteins and nucleic acids. Nucl. Acids. Res.,35, W375-W383. Shapovalov, M.S., ... CP detects both local errors in atomic coordinates and also correctly matches an amino acid sequence to its native three ... It is useful in homology modeling and protein design. A version of the plot (CPint) has also been built and made available to ... It is based on a probabilistic representation of preferred amino acid side-chain orientation, analogous to the preferred ...

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

SINEs are known to share sequence homology with LINES which gives a basis by which the LINE machinery can reverse transcribe ... Vassetzky NS, Kramerov DA (January 2013). "SINEBase: a database and tool for SINE analysis". Nucleic Acids Research. 41 ( ... For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the ... The body of SINEs possess an unknown origin but often share much homology with a corresponding LINE which thus allows SINEs to ...

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

2006). "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID ... which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein that belongs to the L18P ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2001). "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs ...

https://en.wikipedia.org/wiki/Mitochondrial_ribosomal_protein_L18

Nucleic Acids Research. 46 (D1): D447-D453. doi:10.1093/nar/gkx1041. PMC 5753239. PMID 29106644. Hochstrasser M (March 2009). " ... UBLs that are capable of conjugation (sometimes known as Type I) have a characteristic sequence motif consisting of one to two ... Haas AL, Ahrens P, Bright PM, Ankel H (August 1987). "Interferon induces a 15-kilodalton protein exhibiting marked homology to ... Nucleic Acids Research. 39 (8): 3204-23. doi:10.1093/nar/gkq1228. PMC 3082918. PMID 21169198. Hennell James R, Caceres EF, ...

https://en.wikipedia.org/wiki/Ubiquitin-like_protein

Nucleic Acids Res. 27 (17): 3494-502. doi:10.1093/nar/27.17.3494. PMC 148593. PMID 10446239. Ko L, Cardona GR, Chin WW (May ... Jin S, Kharbanda S, Mayer B, Kufe D, Weaver DT (October 1997). "Binding of Ku and c-Abl at the kinase homology region of DNA- ... "Targeted next-generation sequencing for molecular diagnosis of endometriosis-associated ovarian cancer". J. Mol. Med. 94 (7): ... The DNA-Pkcs protein is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids. DNA-PKcs ...

https://en.wikipedia.org/wiki/DNA-PKcs

... that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence ... This homology can be detected by gene or genome sequencing but also by FISH. For instance, human and chimpanzee chromosomes are ... "Observations on chromosome-specific sequencing for the construction of cross-species chromosome homology maps and its ... Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ...

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

... nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... sequence (biology) - sequence homology - sequence motif - sequencing - serine - serotonin - serotonin receptor - serpin - ... It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and ...

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

Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; ... Nucleic Acids Res. 7 (8): 2369-85. doi:10.1093/nar/7.8.2369. PMC 342390. PMID 523320. Friesen WJ, Dreyfuss G (2000). "Specific ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2005). "ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4 ...

https://en.wikipedia.org/wiki/LSM4

... categorized according to sequence homology. The list also includes selected family members that lack human orthologs (NRNC ... Nucleic Acids Research. 25 (10): 1903-12. doi:10.1093/nar/25.10.1903. PMC 146682. PMID 9115356. Rual, Jean-François; Venkatesan ... Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and ... Two putative orphan receptors, HNF4 and USP were found, via structural and mass spectrometry analysis, to bind fatty acids and ...

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

Kudo S, Mattei MG, Fukuda M (1995). "Characterization of the gene for dbpA, a family member of the nucleic-acid-binding ... Kolluri R, Kinniburgh AJ (1991). "Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein". Nucleic ... 1989). "Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology". Gene. ... 1996). "Structural and functional analysis of the human Y-box binding protein (YB-1) gene promoter". Nucleic Acids Res. 24 (10 ...

https://en.wikipedia.org/wiki/Y_box_binding_protein_1

Nucleic Acids Research. 30 (2): 475-81. doi:10.1093/nar/30.2.475. PMC 99834. PMID 11788710. Di Croce L, Raker VA, Corsaro M, ... Fuks F, Burgers WA, Godin N, Kasai M, Kouzarides T (May 2001). "Dnmt3a binds deacetylases and is recruited by a sequence- ... There exists a 98% homology between human and murine homologues. Due to splicing, there exist two main murine RNA isoforms, ... Nucleic Acids Research. 27 (11): 2291-8. doi:10.1093/nar/27.11.2291. PMC 148793. PMID 10325416. Yang L, Rau R, Goodell MA (2015 ...

https://en.wikipedia.org/wiki/DNA_(cytosine-5)-methyltransferase_3A

The amplification refractory mutation system (ARMS)". Nucleic Acids Res. 17 (7): 2503-2516. doi:10.1093/nar/17.7.2503. PMC ... Of this sequence, at least 15 base pairs should be homologous to the target sequence at both the 5' and 3' ends to provide ... to use the linear DNA flanked by homologous regions specific to the cleaved location as a template to rebuild using homology ... In this system, sequences matching foreign bacteriophage or plasmid DNA are incorporated as "spacer" sequences into the ...

https://en.wikipedia.org/wiki/No-SCAR_(Scarless_Cas9_Assisted_Recombineering)_Genome_Editing

... which consists of a conserved 6-amino acid sequence of the following formula: YxLxP, where "x" can be any amino acid ... Nucleic Acids Research. 24 (7): 1294-303. doi:10.1093/nar/24.7.1294. PMC 145771. PMID 8614633. Bilaud T, Brun C, Ancelin K, ... The TERF Homology Domain (TRFH; InterPro: IPR013867) is an area that helps to promote homodimerization of TERF2 with itself. ... the client proteins specific for TERF1 contain the TRFH binding motif sequence of FxLxP, where the amino acid Y (tyrosine) is ...

https://en.wikipedia.org/wiki/Telomeric_repeat-binding_factor_2

1989). "Human prostatic acid phosphatase: cDNA cloning, gene mapping and protein sequence homology with lysosomal acid ... "Nucleotide sequence of human prostatic acid phosphatase determined from a full-length cDNA clone". Nucleic Acids Res. 18 (16): ... Sharief FS, Li SS (1994). "Nucleotide sequence of human prostatic acid phosphatase ACPP gene, including seven Alu repeats". ... 1988). "Molecular cloning and sequence analysis of cDNA encoding human prostatic acid phosphatase". FEBS Lett. 236 (2): 275-81 ...

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

Nucleic Acids Research. 42 (D1): D490-D495. doi:10.1093/nar/gkt1178. ISSN 0305-1048. PMC 3965031. PMID 24270786. "Glycoside ... The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases. This family also includes ... Homology with human alpha-galactosidase A suggests evolution from a common ancestral gene". J. Biol. Chem. 265 (35): 21859- ... Aslanidis C, Schmid K, Schmitt R (1989). "Nucleotide sequences and operon structure of plasmid-borne genes mediating uptake and ...

https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_36

Nucleic Acids Res. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID 16381901. v t e (Genes on human ... Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. ... also have C-terminal regions that share homology with neurotrophin receptors (see NTRK1). SLITRKs are expressed predominantly ...

https://en.wikipedia.org/wiki/SLITRK6

Häsler J, Strub K (2006). "Alu elements as regulators of gene expression". Nucleic Acids Research. 34 (19): 5491-7. doi:10.1093 ... The following table illustrates the sequence similarity between human c10orf76 protein and various orthologs. Similar sequences ... Jia CY, Nie J, Wu C, Li C, Li SS (Aug 2005). "Novel Src homology 3 domain-binding motifs identified from proteomic screen of a ... Nucleic Acids Research. 35 (21): 7303-12. doi:10.1093/nar/gkm847. PMC 2175361. PMID 17959645. "NCBI BLAST Tool". Retrieved 2 ...

https://en.wikipedia.org/wiki/ARMH3

An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid- ... The K Homology (KH) domain is a protein domain that was first identified in the human heterogeneous nuclear ribonucleoprotein ( ... The nucleic acid is bound in an extended conformation across one side of the domain. The binding occurs in a cleft formed ... Grishin NV (February 2001). "KH domain: one motif, two folds". Nucleic Acids Res. 29 (3): 638-43. doi:10.1093/nar/29.3.638. PMC ...

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

Nucleic Acids Research. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. Farag IF, Youssef NH, ... The non-homology of the genes downstream of LOOT RNAs makes this scenario less likely. However, the number of different gene ... but the existence of the bacterial phylum is known only through analysis of metagenomic sequences. Curiously, the LOOT motif is ...

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

Adkar-Purushothama CR, Perreault JP (August 2020). "Impact of Nucleic Acid Sequencing on Viroid Biology". International Journal ... "Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms ... Although viroids are composed of nucleic acid, they do not code for any protein. The viroid's replication mechanism uses RNA ... and nucleic acid hybridization has allowed for rapid and inexpensive detection of known viroids in biosecurity inspections, ...

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

The third K/R editing site within the coding sequence is found at amino acid position 15 of the final protein where a Lysine is ... Nucleic Acids Research. 33 (4): 1162-8. arXiv:q-bio/0502045. Bibcode:2005q.bio.....2045L. doi:10.1093/nar/gki239. PMC 549564. ... Although database searches revealed no homology to any human gene at the time of identification, mouse, rat and zebrafish ... Exon 1 of the gene encodes a 5′ sequence of the 5′UTR while exon 2 includes the remaining sequence of the 5′UTR, the coding ...

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

Momand J, Jung D, Wilczynski S, Niland J (August 1998). "The MDM2 gene amplification database". Nucleic Acids Research. 26 (15 ... in seven candidate bacterial phyla and in one archaeon The sequences of the Pup homologs are very different from the sequences ... and the two families share no homology. In contrast to the three-step reaction of ubiquitination, pupylation requires two steps ... Journal of Nucleic Acids. 2010: 1-8. doi:10.4061/2010/761217. PMC 2935186. PMID 20847899. Jackson SP, Durocher D (March 2013 ...

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

Haft, DH; Selengut, JD; White, O (2003). "The TIGRFAMs database of protein families". Nucleic Acids Research. 31 (1): 371-3. ... Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment. Sequences that score ... Eddy, SR (2009). "A new generation of homology search tools based on probabilistic inference". Genome Informatics. ... 2021). "RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation". Nucleic Acids ...

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

Hybrid Fusion protein Gene pool Gene flow Introgression Nucleic acid hybridization Mouse models of breast cancer metastasis " ... a protein coding sequence (usually derived from the cDNA for the protein of interest), and a stop sequence. These are typically ... Transgenic cattle with an increased muscle phenotype has been produced by overexpressing a short hairpin RNA with homology to ... Transgene describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into ...

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

Nucleic Acids Res. 14 (19): 7817. doi:10.1093/nar/14.19.7817. PMC 311807. PMID 2877435. Norment AM, Littman DR (1989). "A ... Parnes JR, Sizer KC, Sukhatme VP, Hunkapiller T (1986). "Structure of Leu-2/T8 as deduced from the sequence of a cDNA clone". ... Both alpha and beta chains share significant homology to immunoglobulin variable light chains. This gene encodes the CD8 alpha ... Littman DR, Thomas Y, Maddon PJ, Chess L, Axel R (1985). "The isolation and sequence of the gene encoding T8: a molecule ...

https://en.wikipedia.org/wiki/CD8A

Homology modeling can be used to construct an atomic-resolution model of the "target" integral protein from its amino acid ... Nucleic Acids Res. 37 (Database issue): D274-8. doi:10.1093/nar/gkn862. PMC 2686586. PMID 19022853. "Integral membrane proteins ... 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. ...

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

... sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.. Nucleic ... Acids Res. 43(Database issue):D300-5.*PubMed. *Google Scholar. Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender ... Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into ...

https://www.ncbs.res.in/publications?page=3&%3Bamp%3Bs=title&%3Bamp%3Bo=asc&%3Bamp%3Bf%5Bauthor%5D=1255&%3Bf%5Bauthor%5D=973&f%5Bauthor%5D=207&s=year&o=desc

Sequence Homology, Nucleic Acid * Transcription Initiation Site * WNK Lysine-Deficient Protein Kinase 1 ...

https://pubmed.ncbi.nlm.nih.gov/14645531/

... there is no nucleic acid sequence homology between Reovirus members and members of other genera [21] . At present, there are 12 ... The orbiviruses are distinguished from the reoviruses by acid lability, slight solvent sensitivity, serology (CF and HI), and ...

https://wwwn.cdc.gov/Arbocat/VirusDetails.aspx?ID=68&SID=5

... was positive for evidence of rabies virus nucleic acid. Sequence analysis demonstrated 100% homology with a rabies virus ...

http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5302a4.htm

... sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.. Nucleic ... Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into ... Acids Res. 43(Database issue):D300-5.*PubMed. *Google Scholar. S. Metri R, Hariharaputran S, Ramakrishnan G, Anand P, ...

https://www.ncbs.res.in/publications?page=5&%3Bamp%3Bs=author&%3Bamp%3Bo=asc&%3Bamp%3Bf%5Bauthor%5D=369&%3Bf%5Bauthor%5D=228&f%5Bauthor%5D=207&s=title&o=asc

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. 289-294. ... PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. 266-268. *Goran Neshich, ... Nucleic Acids Research, Volume 33. Volume 33, Database-Issue, January 1 2005. Editorials: *Alex Bateman: Editorial. 1. *Dov ... NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 501-504. * ...

https://vldb.org/dblp/db/journals/nar/nar33.html

The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology. Nucleic Acids ... N-terminal amino acid sequencing. The N-terminal amino acid sequence was determined by the method of Matsudaira (1987). Briefly ... The phylogenetic tree representing the multiple sequence alignment for the full-length deduced amino acid sequences of Wap65s ... The deduced amino acid sequence of mWap65-1 showed 66-68% identity with those of goldfish Wap65 (Kikuchi et al., 1995), carp ...

https://journals.biologists.com/jeb/article/207/8/1387/15080/The-occurrence-of-two-types-of-hemopexin-like

Wengler G., Wengler G., Gross H. J. 1978; Studies on virus-specific nucleic acids synthesized in vertebrate and mosquito cells ... Gould A. R., Symons R. H. 1977; Determination of the sequence homology between the four RNA species of cucumber mosaic virus by ... Gonda T. J., Symons R. H. 1978; The use of hybridization analysis with complementary DNA to determine the RNA sequence homology ... Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A) Donald B. Smith, Jacques ...

https://www.microbiologyresearch.org/content/journal/jgv/10.1099/0022-1317-65-12-2173

... showed the highest degree of identity among their amino acid sequences (58%). The analysis of conserved and exposed residues ... 3D models of lipocalins not reported in the protein data bank were modeled by homology to identify potential antigenic regions ... The amino acid sequences of several lipocalins from different domestic animals (mouse, dog, cat, bull, hamster, horse and pig) ... A Multiple Sequence Alignment Toolbox That Integrates Homology-Extended and Secondary Structure Information. Nucleic Acids ...

https://file.scirp.org/Html/1-1410213_89346.htm

2004) [email protected]: a web server for combining sequences and structures into a multiple sequence alignment Nucleic Acids ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... 2006) Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee Nucleic Acids ... and positioned in relation to the Gorab amino acid sequence. The Y-axis shows fraction of deuteration compared to maximum level ...

https://elifesciences.org/articles/57241

... establishing the basis for loop homology modeling. Nucleic Acids Research 38 (3), pp. 970 - 980 (2010) ... Schudoma, C.; May, P.; Walther, D.: Modeling RNA loops using sequence homology and geometric constraints. Bioinformatics 26 (13 ... Schudoma, C.; Larhlimi, A.; Walther, D.: The influence of the local sequence environment on RNA loop structures. Rna-a ... Schudoma, C.; May, P.; Nikiforova, V.; Walther, D.: Sequence-structure relationships in RNA loops: ...

https://www.mpimp-golm.mpg.de/publication-search/1357523?person=%2Fpersons%2Fresource%2Fpersons97397

Frith MC: A new repeat-masking method enables specific detection of homologous sequences. Nucleic Acids Res 2011, 39:e23. ... Frith MC: Gentle masking of low-complexity sequences improves homology search. PLoS One 2011, 6:e28819. ... Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580. ... Long read sequencing and mapping to the reference genome. We used 21 long read whole genome sequencing datasets, from 21 humans ...

https://www.researchsquare.com/article/rs-79348/v1

Nucleic acid sequence homology (finding). Code System Preferred Concept Name. Nucleic acid sequence homology (finding). ...

https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=74354009

Nucleic Acid. Homologs, Nucleic Acid Sequence. Homology, Base Sequence. Homology, Nucleic Acid Sequence. Nucleic Acid Sequence ... Base Sequence Homology Homologies, Base Sequence Homology, Base Sequence Homology, Nucleic Acid Sequence Nucleic Acid Sequence ... Nucleic Acid Sequence Homology. Sequence Homologies, Base. Sequence Homology, Base. Tree number(s):. G02.111.810.550. G05.810. ... Sequence Homologies, Base Sequence Homology, Base Homologous Sequences, Nucleic Acid - Related but not broader or narrower ...

https://decs.bvsalud.org/en/ths/resource/?id=23515

... to arachidonic acid (AA) and in the conversion of 20:4n-3 to eicosapentaenoic acid (EPA). Delta-6 desaturase may be used, for ... In particular, &Dgr;5-desaturase may be utilized, for example, in the conversion of dihomo-&ggr;-linolenic acid (DGLA) ... example, in the conversion of linoleic (LA) to &ggr;-linolenic acid (GLA). AA or polyunsaturated fatty acids produced therefrom ... The subject invention relates to the identification of genes involved in the desaturation of polyunsaturated fatty acids at ...

https://patents.justia.com/patent/20030157144

6 Sequence Homology, Amino Acid. *6 Sequence Homology, Nucleic Acid. *5 DNA Mutational Analysis ...

https://imsear.searo.who.int/handle/123456789/114201/simple-search?query=&sort_by=score&order=desc&rpp=10&filter_field_1=dateIssued&filter_type_1=equals&filter_value_1=%5B2000+TO+2009%5D&filter_field_2=subject&filter_type_2=equals&filter_value_2=Molecular+Sequence+Data&etal=0&filtername=subject&filterquery=Base+Sequence&filtertype=equals

Filters: Keyword is Sequence Homology, Nucleic Acid and Author is Alan T Bakalinsky [Clear All Filters] ...

https://horticulture.oregonstate.edu/biblio?f%5Bkeyword%5D=3586&f%5Bauthor%5D=23976&s=title&o=asc

Sequence Homology, Nucleic Acid. R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., ... Sequence Homology, Amino Acid. R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., ... Sequence Homology. K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., ... "Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.*Google Scholar ...

https://lsi.princeton.edu/research/publications?f%5Bkeyword%5D=S&f%5Bauthor%5D=184&s=keyword&o=asc

SHERLOCK: nucleic acid detection with CRISPR nucleases. Kellner Max J et al. Nature protocols 2019 Oct (10) 2986-3012 * ... Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. Ali Raja Hashim et al. Molecular biology ... Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden. Sacchini Lorena et al ... Bit-parallel sequence-to-graph alignment. Rautiainen Mikko et al. Bioinformatics (Oxford, England) 2019 Oct (19) 3599-3607 * ...

https://phgkb.cdc.gov/PHGKB/amdClip.action?action=archive&date=10/03/2019

Nucleotide sequence homology requirements of HIV-1-specific short hairpin RNA. Nucleic Acids Res. 2003. 31. 6444. 6449. 10.1093 ... Nucleic Acids Res. 2004. 32. 4776. 4785. 10.1093/nar/gkh824. 15356295. Bernstein. E. Caudy. AA. Hammond. SM. Hannon. GJ. Role ... Nucleic Acids Res. 2006. 34. 4206. 4215. 10.1093/nar/gkl460. 16935882. Fukuda. T. Yamagata. K. Fujiyama. S. DEAD-box RNA ... termed the seed sequence, and the target mRNAs [. 16. ,. 17. ]. A recent study appears to oppose this seed sequence pairing ...

https://stacks.cdc.gov/view/cdc/3556/cdc_3556_DS6.txt

DIALIGN is a program for aligning multiple protein or nucleic acid sequences. It constructs alignments by comparing entire ... but it is most successful when sequences share only local homologies. DIALIGN is available as a download, a web console, and a ... segments of the sequences. This method can be used for both global and local alignment, ...

https://www.programmableweb.com/api/dialign-rest-api-v10/developers

Molecular sequence data (1). *Nucleic acid repetitive sequences (1). *Nucleic acid sequence homology (1) ...

https://archive-ouverte.unige.ch/documents/facets/sort:Document.year/direction:asc?newFacet=subjectFacet%3DBacterial+Genome

Comparative genomic sequence analysis and isolation of human and mouse alternative EGFR transcripts encoding truncated receptor ... Sequence Analysis, DNA * Sequence Homology, Nucleic Acid * Tissue Distribution * Transfection * Translocation, Genetic ... Comparative genomic sequence analysis and isolation of human and mouse alternative EGFR transcripts encoding truncated receptor ... This study presents the annotated genomic sequence and exon-intron organization of the human and mouse epidermal growth factor ...

https://vivo.library.tamu.edu/vivo/display/n79770SE

... a procedure to find homologies among many sequences, Nucleic Acids Research, 14(1), 1986, 543-550. DOI:10.1093/nar/14.1.543 M. ... J. V. Maizel, R. P. Lenk: Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences, Proceedings of the National ... Dot plot, Dot matrix, Graphic matrix, Link plot, Sequence matrix (recurrence of symbols) genome sequence alignment, structures ... map of contacts of protein sequences) investigation of protein folding H. S. Chan, K. A. Dill: Intrachain loops in polymers: ...

http://www.recurrence-plot.tk/related_methods.php

Nucleic Acids Res., 40 (Web Server issue): W140-6. *F Dreher et al (2012) DIPSBC - Data Integration Platform for Systems ... Construction of a pig physical interactome using a sequence homology and a comprehensive reference human interactome. Evol ... Nucleic Acids Res., 37 (Database issue): D623-8. *A Rasche, H Al-Hasani, R Herwig (2008) Meta-analysis approach identifies ... Nucleic Acids Res. 39 (Database issue): D712-7. *K Pentchev, K Ono, R Herwig, T Ideker, A Kamburov (2010) Evidence mining and ...

https://www.molgen.mpg.de/3475941/herwig_publications

Us9 has no obvious homology to any protein or nucleic acid sequences in GenBank that might provide insight into how it ... A) The amino acid sequence of PRV Us9. Amino acids that have been substituted with alanine are bolded. The acidic region of Us9 ... A) The amino acid sequence of PRV Us9. Amino acids that have been substituted with alanine are bolded. The acidic region of Us9 ... 1 for amino acid sequence of Us9 and location of the alanine substitution mutations) (Brideau et al., 2000a,b). PRV 91 (gE-null ...

https://rupress.org/jcb/article/154/4/741/32242/A-conserved-herpesvirus-protein-necessary-for

The identification of this clone as chick CNTFR alpha was based on the homology in amino acid sequence (approximately 70%) with ... The isolated cDNA clone contained a approximately 2-kb insert with an open reading frame of 362 amino acids. ... Sequence Homology, Nucleic Acid. *Spinal Cord. *Transcription, Genetic. Differential expression of ciliary neurotrophic factor ...

http://transhumanist.ru/CNTFR

Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (bvsalud.org)
We analysed a collection of 336 diverse pneumococcal genomes dating from 1916 onwards, identified bacteriocin cassettes, detailed their genetic composition and sequence diversity, and evaluated the data in the context of the pneumococcal population structure. (ox.ac.uk)
The Tsa56 gene was obtained for sequencing, and the homology and phylogenetic analyses showed that CX1601 and CX1604 shared high homology and close genetic relationship with the Kato strains of Ot, while CX1602 and CX1603 were highly homologous and closely related to Gilliam strains, but relatively low homology and large genetic distances with other strains. (bmsw.net.cn)
Because a triplet is the length of a gene codon, we speculate that the structural physics of nucleic acids may have biased the evolution of recombinase proteins to exploit triplet base stacks and also the genetic code. (ox.ac.uk)
Furthermore, increased knowledge about the genetic and molecular basis of life has revealed many major exceptions and contradictions to the theory which, as a result, have largely negated homology as a proof of evolution. (creation.com)
Scientists use these reagents for various reasons - for example, to study the function of a given gene or genetic sequence in a disease - and if the sequences are wrongly reported it could affect the reproducibility of the research. (cdc.gov)

Comparative genomic sequence analysis and isolation of human and mouse alternative EGFR transcripts encoding truncated receptor isoforms. (tamu.edu)
This study presents the annotated genomic sequence and exon-intron organization of the human and mouse epidermal growth factor receptor (EGFR) genes located on chromosomes 7p11.2 and 11, respectively. (tamu.edu)
Genomic (nucleic acid) vaccines. (who.int)
Chromatin immunoprecipitation combined with the next-generation DNA sequencing technologies (ChIP-seq) becomes a key approach for detecting genome-wide sets of genomic sites bound by proteins, such as transcription factors (TFs). (biomedcentral.com)
He also noted concern regarding delays in referring specimens to the laboratory for testing, and emphasized the need for improvement in timeliness of reporting and tracking of the viruses referred for genomic sequencing. (who.int)
He thanked the regional and global specialized laboratories for their efforts to provide timely results of the genomic sequencing of wild polioviruses, and for their help in planning and monitoring polio eradication activities in the Region. (who.int)

genome sequence alignment, structures of proteins (cp. (recurrence-plot.tk)
Most evolutionary analyses or structure modeling are based upon pre-estimated multiple sequence alignment (MSA) models. (peerj.com)
Hence, increasing or identifying signal inside sequence alignment has intensified over the last few years. (peerj.com)
We show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. (peerj.com)
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. (peerj.com)
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. (peerj.com)
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. (peerj.com)
Bit-parallel sequence-to-graph alignment. (cdc.gov)
After the best-fit template is selected, the structural model of the sequence is built based on the alignment with the chosen template. (wikimili.com)
Threading alignment: Align the target sequence with each of the structure templates by optimizing the designed scoring function. (wikimili.com)
This method can be used for both global and local alignment, but it is most successful when sequences share only local homologies. (programmableweb.com)
Sequence alignment showed that an additional exon, which is present only in the mRNA of GAGE-1, has been disrupted in gene GAGE-7B by the insertion of a long interspersed repeated element retroposon. (ox.ac.uk)
Multiple sequence alignment (MSA) was used to locate the conserved residues. (avensonline.org)

A nested, reverse transcription polymerase chain reaction assay performed on saliva samples was positive for evidence of rabies virus nucleic acid. (cdc.gov)
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. (ox.ac.uk)
Transcription factors recognize and bind to specific DNA sequences (named motifs, typically about 5~20 base-pair (bp) long) [ 18 , 19 ]. (biomedcentral.com)

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. (vldb.org)
Molecular cloning of seven mouse immunoglobulin K chain messenger ribonucleic acids. (microbiologyresearch.org)
To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. (huji.ac.il)
However, the molecular epidemiologic analysis, which included extended sequencing, strongly suggested that all cases derived from a single importation of measles virus genotype D4. (cdc.gov)
Eight StCRK members were identified, with amino acid size from 459 to 686 aa, molecular weight of 50.75-77.50 kD, and isoelectric point of 5.84-8.75. (chinacrops.org)
1995). Diisocyanates and acid anhydrides cyanates has a low association with atopy, low prevalence are among the most common low molecular weight (LMW) with specific IgE antibodies and a mixed Th1-Th2 response classes of chemicals responsible for occupational asthma. (cdc.gov)

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. (cdc.gov)
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. (vldb.org)
The members of this family have been characterized according to their sequence or structure, including a large number of proteins. (scirp.org)
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. (peerj.com)
It differs from the homology modeling method of structure prediction as it (protein threading) is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do. (wikimili.com)
Superfamily (probable common evolutionary origin): Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable, are placed together in superfamilies. (wikimili.com)
We here propose that the structural distortion represented by Σ-DNA, which is thus physically inherent to the nucleic acid, is related to how recombination proteins mediate recognition of sequence homology and execute strand exchange. (ox.ac.uk)
Proteins of the ets proto-oncogene family bind to similar sequences and we have found that a member of this family, Elk-1, forms SRF-dependent ternary complexes with the SRE. (cnrs.fr)
Elk-1 and p62TCF have the same DNA sequence requirements and antibodies against Elk-1 block the binding of both proteins. (cnrs.fr)
A number of actin-binding proteins, including spectrin, alpha-actinin and fimbrin, contain a 250 amino acid stretch called the actin binding domain (ABD). (embl.de)
This guideline suggested the assessment ranging from the source of novel proteins, similarities of the target proteins to known allergens at the primary protein sequence level, the physicochemical properties, and protein abundance etc. (biomedcentral.com)
Although, providing the massive amount of data by recent genome sequencing projects but many of these genomes are still not fully annotated as well as consist of genes/proteins with unknown function and structure. (avensonline.org)
Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. (cam.ac.uk)

We performed a genome-wide survey of the millions of human tandem repeats using publicly available long read genome sequencing data from 21 humans. (researchsquare.com)
Darwin built his case mostly on anatomical comparisons revealing homology between humans and apes. (creation.com)

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. (ncbs.res.in)
DDBJ in collaboration with mass-sequencing teams on annotation. (vldb.org)

The EMBL Nucleotide Sequence Database. (vldb.org)
Nucleotide sequences in DNA. (akjournals.com)
Since the only constraint for TALEN binding is that the first nucleotide in each target sequence is a T, sites exist almost everywhere in the genome. (wormbook.org)

S4: structure-based sequence alignments of SCOP superfamilies. (vldb.org)
Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. (cdc.gov)
It constructs alignments by comparing entire segments of the sequences. (programmableweb.com)

Compilation of tRNA sequences and sequences of tRNA genes. (vldb.org)
The subject invention relates to the identification of genes involved in the desaturation of polyunsaturated fatty acids at carbon 5 (i.e. (justia.com)
In view of these difficulties, it is of significant interest to isolate genes involved in PUFA synthesis from species that naturally produce these fatty acids and to express these genes in a microbial, plant, or animal system which can be altered to provide production of commercial quantities of one or more PUFAs. (justia.com)
Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). (duke.edu)
However, the presence of a PbGR2 splice variant that lacks this insert, as well as the loss of the exon encoding these amino acids in the genes encoding for other teleost GR2 suggests the selection of two receptors with different DNA-binding domain structures in teleosts. (biomedcentral.com)
Comparison of the human and mouse erythropoietin genes shows extensive homology in the flanking regions. (ox.ac.uk)
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. (ox.ac.uk)
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. (ox.ac.uk)
To identify putative candidate genes for IDDM4, we have constructed a 400-kb clone contig in this region and sequenced the clones. (ox.ac.uk)
Detailed sequence analysis has identified a further three genes in this region: the CGI-85 gene (previously identified by W.-C. Lin) and two novel genes, C11orf24 and C11orf23. (ox.ac.uk)
The expressed sequence tags (ESTs), hormones and genes responsible for regulating wood formation were identified in Populu s increasingly [7, 8, 9]. (researchsquare.com)

The amino acid sequences of several lipocalins from different domestic animals (mouse, dog, cat, bull, hamster, horse and pig) were used to determine the degree of kinship by phylogenetic studies. (scirp.org)
Homology and phylogenetic analyses were performed using bioinformatics software. (bmsw.net.cn)
Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. (biomedcentral.com)

The use of hybridization analysis with complementary DNA to determine the RNA sequence homology between strains of plant viruses: its application to several strains of cucumoviruses. (microbiologyresearch.org)
Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (cdc.gov)
DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. (biomedcentral.com)

Determination of the sequence homology between the four RNA species of cucumber mosaic virus by hybridization analysis with complementary DNA. (microbiologyresearch.org)

The encoded mouse P2X3 protein consists of 397 amino acids and shows 99% identity with rat P2X3. (ox.ac.uk)
A splice variant of PbGR2 produces an isoform that lacked these 9 amino acids (PbGR2b). (biomedcentral.com)
The first computational approach proposed by the consultation group of FAO/WHO in 2001, defined a possible allergenic protein with the exact match a stretch of six or more consecutive identical amino acids (rule 1) or more than 35% identity within any window of 80 amino acids in comparison with any known allergen (rule 2) [ 6 ]. (biomedcentral.com)

Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. (cdc.gov)
Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. (cdc.gov)
We designed a liquid biopsy (LB) platform employing low-pass whole genome sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA from plasma to detect genome-wide copy number alterations (CNAs) and gene fusions in pediatric solid tumors. (cdc.gov)
To gain more insight into the etiology of these mesenchymal tumors, A new study carried out whole-genome germline sequencing on 1,644 individual people, along with family members and matched control participants. (cdc.gov)

Considerable insights into important cis regulatory elements in a gene can be gleaned from the identification of sequence homologies among different species. (ox.ac.uk)
Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. (huji.ac.il)
The sequences of the studied specimens were compared with 18 barcodes of this species from Barcode of Life Datasystems (BOLD). (huji.ac.il)
Despite approximately 99% identity at the level of DNA sequence, however, recombination hotspots were found rarely (if at all) at the same positions in the two species, and no correlation was observed in estimates of fine-scale recombination rates. (ox.ac.uk)
5 An early example of how homology was used to argue for macroevolution is a 1928 biology text which, in answer to the question 'Why do the individuals in a species have all of their parts homologous? (creation.com)
Biologists carry this answer a step further and say that since homology within the species is the result of common ancestry therefore all homology is due to common ancestry and the closeness of relationship determines the number of homologous parts [emphasis in original]. (creation.com)

Thus, local patterns of recombination rate have evolved rapidly, in a manner disproportionate to the change in DNA sequence. (ox.ac.uk)

G. Krishnan, R. K. Kaul, P. Jagadeeswaran: DNA sequence analysis: a procedure to find homologies among many sequences, Nucleic Acids Research, 14(1), 1986, 543-550. (recurrence-plot.tk)

Sequence analysis demonstrated 100% homology with a rabies virus variant associated with the silver-haired bat ( Lasionycteris noctivagans ). (cdc.gov)
J. V. Maizel, R. P. Lenk: Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences, Proceedings of the National Academy of Sciences, 78(12), 1981, 7665-7669. (recurrence-plot.tk)
MEDIPS: Genome wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. (mpg.de)
Initial sequencing and analysis of the human genome. (akjournals.com)
Fluorescence detection in automated DNA sequence analysis. (akjournals.com)
Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. (akjournals.com)
We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile . (biomedcentral.com)

taking monodentate particles to green acid: Why cost hours, ' Department of Chemistry, University of Pennsylvania, October 18, 2001. (valleybay.com)

The second part, homology and evolutionary modeling are the most common applications of MSAs. (peerj.com)
Does homology provide evidence of evolutionary naturalism? (creation.com)
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. (creation.com)
Sequence similarity was brought in through Protein Data Bank and non-redundant database using BLASTp program of NCBI and a search for templates revealed that yjaB shares 97% homology to a protein of Escherichia coli, indicating this protein is evolutionary conserved and was found with acetyltransfarase. (avensonline.org)
Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. (biomedcentral.com)

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. (vldb.org)
3D models of lipocalins not reported in the protein data bank were modeled by homology to identify potential antigenic regions compromised in the cross-reactivity of this group of allergens. (scirp.org)
mouse B7-Ag, chromosome 4, between Dsil and D4Nds16) and sequence homology in the promoter regions which strongly suggests that B7-Ag is the mouse homologue of CD52. (ox.ac.uk)

The influence of the local sequence environment on RNA loop structures. (mpg.de)
Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model. (wikimili.com)
This generally involves selecting protein structures from databases such as PDB , FSSP , SCOP , or CATH , after removing protein structures with high sequence similarities. (wikimili.com)
The design of the scoring function: Design a good scoring function to measure the fitness between target sequences and templates based on the knowledge of the known relationships between the structures and the sequences. (wikimili.com)
According to Darwin' theory of common descent, the structures that we call homologies represent characteristics inherited with some modification from a corresponding feature in a common ancestor. (creation.com)

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (ncbs.res.in)
SHERLOCK: nucleic acid detection with CRISPR nucleases. (cdc.gov)
Country": "XG", "Code": "Probe", "Name": "Probe" }, { "Language": "en", "Value": "The RNA Process Control Kit LSR contains a nuclease-resistant RNA that can be added at various steps during the nucleic acid purification of viral RNA detection workflows. (roche.com)
Country": "XG", "Code": "Product Description", "Name": "Product Description" }, { "Language": "en", "Value": "Nuclease-resistant Control RNA, Control RNA Detection Mix (Cy5-labeled probe and primers), and LightCycler ® Multiplex RNA Virus Master for monitoring the complete process of virus detection, from sample preparation to RT-qPCR. (roche.com)
Country": "XG", "Code": "Content", "Name": "Content" }, { "Language": "en", "Value": "The RNA Process Control Kit LSR is a tool to control for potential failures of sample preparation, amplification, detection, and handling errors. (roche.com)
DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. (akjournals.com)

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. (vldb.org)
We have also sequenced the orthologous DNA from mouse. (ox.ac.uk)

During the presentation, I would like to share two approaches, homology extension and sampling, on this topic. (peerj.com)
The three most widely used allergen computational prediction approaches including sequence-, motif- and SVM-based (Support Vector Machine) methods were systematically compared using the defined parameters and we found that SVM-based method outperformed the other two methods with higher accuracy and specificity. (biomedcentral.com)
This study comprehensively evaluated sequence-, motif- and SVM-based computational prediction approaches for allergens and optimized their parameters to obtain better performance. (biomedcentral.com)

Nucleic acids research 44, W339-343(2016). (peerj.com)
Nucleic acids research 43, W3-6 (2015). (peerj.com)
Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
Low cost and massively parallel sequencing technologies have revolutionized the area of genomics research in last two decades. (jcbose.ac.in)

We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. (biomedcentral.com)
Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. (biomedcentral.com)

The amino acid sequences of lipocalins from seventeen domestic animals were selected based on allergenic capacity reported. (scirp.org)
It must be noted that animals cannot desaturate beyond the &Dgr;9 position and therefore cannot convert oleic acid into linoleic acid. (justia.com)
Homology involves the theory that macroevolutionary relationships can be proven by the similarity in the anatomy and physiology of different animals. (creation.com)

The use of timely genotype sequencing, rigorous epidemiologic investigation, and a better understanding of the gaps in surveillance are needed to maintain Ontario's measles elimination status. (cdc.gov)

HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. (vldb.org)
Construction of a pig physical interactome using a sequence homology and a comprehensive reference human interactome. (mpg.de)
A map of human genome variation from population-scale sequencing. (mpg.de)
Finally, we have shown that the human, mouse, rat, and chicken 1.8- to 3.0-kb alternative EGFR transcripts are generated by distinct splicing mechanisms and that each of these mRNAs contains unique 3' sequences that are not evolutionarily conserved. (tamu.edu)
The sequence of the human genome. (akjournals.com)
For both the Alt-R CRISPR-Cas9 System and the Alt-R CRISPR-Cas12a (Cpf1) System, we offer recommended products and sequences for guide RNA positive controls that target HPRT in human, mouse, and rat cells. (idtdna.com)

Design PCR primers that amplify your experimental target site and adjacent sequences. (idtdna.com)

In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. (nature.com)

electron-accepting light cultures to mathematical Acne Vulgaris: Why sequences hope to ask minerals, ' Department of Physics, Drexel University, February 7, 2002. (valleybay.com)

Shigella flexneri serotype 5b (strain 8401) was set apart and sequenced from epidemic in China, with compassion provided by the National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention[ 4 ]. (avensonline.org)

The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. (vldb.org)
The prediction is made by "threading" (i.e. placing, aligning) each amino acid in the target sequence to a position in the template structure, and evaluating how well the target fits the template. (wikimili.com)

Highly cited genetics studies found to contain sequence errors. (cdc.gov)

siRNAdb: a database of siRNA sequences. (vldb.org)
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. (vldb.org)
TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension. (peerj.com)

Anatomy10

Organisms23

Chemicals and Drugs85

Analytical, Diagnostic and Therapeutic Techniques and Equipment47

Phenomena and Processes92

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science8

Health Care3

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

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

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

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

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

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

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

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)

Sequence Homology, Amino Acid

Peptide Nucleic Acids

Sequence Homology, Nucleic Acid

Molecular Sequence Data

Amino Acid Sequence

Base Sequence

Cloning, Molecular

Nucleic Acid Hybridization

Nucleic Acid Conformation

DNA

Sequence Homology

Nucleic Acid Probes

Sequence Alignment

Nucleic Acid Amplification Techniques

RNA

Nucleic Acid Denaturation

Escherichia coli

Genes

Models, Molecular

DNA, Complementary

Binding Sites

DNA Restriction Enzymes

DNA, Bacterial

Plasmids

Sequence Analysis, DNA

Oligonucleotides

Restriction Mapping

Polymerase Chain Reaction

Species Specificity

DNA, Viral

Genes, Bacterial

Protein Structure, Tertiary

RNA, Messenger

Protein Binding

Structural Homology, Protein

Bacterial Proteins

Phylogeny

RNA, Viral

src Homology Domains

Protein Conformation

Transcription, Genetic

Cell Line

Molecular Weight

Open Reading Frames

Recombinant Proteins

Mutation

DNA Primers

Proteins

Gene Library

Conserved Sequence

Repetitive Sequences, Nucleic Acid

Substrate Specificity

Kinetics

Multigene Family

Viral Proteins

Genes, Viral

Oligonucleotide Probes

DNA Probes

Carrier Proteins

DNA-Binding Proteins

Oligodeoxyribonucleotides

Chromosome Mapping

Blotting, Southern

DNA, Single-Stranded

Recombinant Fusion Proteins

Electrophoresis, Polyacrylamide Gel

Protein Structure, Secondary

Peptide Fragments

RNA, Bacterial

Peptides

Blotting, Northern

Self-Sustained Sequence Replication

Biological Evolution

Saccharomyces cerevisiae

Structure-Activity Relationship

Crystallography, X-Ray

Cattle

Transfection

Nucleic Acid Heteroduplexes

Membrane Proteins