A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
The functional hereditary units of BACTERIA.
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Proteins found in any species of bacterium.
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).
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A 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.
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).
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.
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.
Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.
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.
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.
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.
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.
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)
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.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Genotypic differences observed among individuals in a population.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
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 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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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).
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The sum of the weight of all the atoms in a 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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
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.
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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The functional hereditary units of VIRUSES.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)
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.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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).
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.
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).
Ribonucleic acid that makes up the genetic material of viruses.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
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.
Proteins prepared by recombinant DNA technology.
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.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
In 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.
Established cell cultures that have the potential to propagate indefinitely.
Proteins found in any species of virus.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
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.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The functional hereditary units of FUNGI.
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
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.
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.
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 polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
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 mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
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 PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The genetic complement of a BACTERIA as represented in its DNA.
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.
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.
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.
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.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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.
Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Transport proteins that carry specific substances in the blood or across cell membranes.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
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 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).
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.
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.
Deoxyribonucleic acid that makes up the genetic material of plants.
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.
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)
Proteins isolated from the outer membrane of Gram-negative bacteria.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
Diseases of plants.
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 sequential location of genes on a chromosome.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
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 genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The rate dynamics in chemical or physical systems.
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.
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.
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.
Procedures for identifying types and strains of fungi.
A country spanning from central Asia to the Pacific Ocean.
Proteins that form the CAPSID of VIRUSES.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Proteins found in any species of fungus.
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
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.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
Proteins obtained from ESCHERICHIA COLI.
Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).
A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.
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.
The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.
A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Nucleic acid sequences involved in regulating the expression of genes.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.
Life or metabolic reactions occurring in an environment containing oxygen.
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.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
A genus of asporogenous bacteria that is widely distributed in nature. Its organisms appear as straight to slightly curved rods and are known to be human and animal parasites and pathogens.
The functional hereditary units of PLANTS.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
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.
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.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
Deoxyribonucleic acid that makes up the genetic material of protozoa.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
A ubiquitous sodium salt that is commonly used to season food.
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)
Actual loss of portion of a chromosome.
Refuse liquid or waste matter carried off by sewers.
Deoxyribonucleic acid that makes up the genetic material of archaea.
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.
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.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.

The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. (1/5206)

We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyces cerevisiae, the 0.8-MDa ADA complex and the 1.8-MDa SAGA complex. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex contains several subunits which also function as part of other protein complexes, including a subset of TATA box binding protein-associated factors (TAFIIs) and Tra1. These observations raise the question of whether the 0.8-MDa ADA complex is a subcomplex of SAGA or whether it is a distinct HAT complex that also shares subunits with SAGA. To address this issue, we sought to determine if the ADA complex contained subunits that are not present in the SAGA complex. In this study, we report the purification of the ADA complex over 10 chromatographic steps. By a combination of mass spectrometry analysis and immunoblotting, we demonstrate that the adapter proteins Ada2, Ada3, and Gcn5 are indeed integral components of ADA. Furthermore, we identify the product of the S. cerevisiae gene YOR023C as a novel subunit of the ADA complex and name it Ahc1 for ADA HAT complex component 1. Biochemical functions of YOR023C have not been reported. However, AHC1 in high copy numbers suppresses the cold sensitivity caused by particular mutations in HTA1 (I. Pinto and F. Winston, personal communication), which encodes histone H2A (J. N. Hirschhorn et al., Mol. Cell. Biol. 15:1999-2009, 1995). Deletion of AHC1 disrupted the integrity of the ADA complex but did not affect SAGA or give rise to classic Ada(-) phenotypes. These results indicate that Gcn5, Ada2, and Ada3 function as part of a unique HAT complex (ADA) and represent shared subunits between this complex and SAGA.  (+info)

Inhibition of src family kinases by a combinatorial action of 5'-AMP and small heat shock proteins, identified from the adult heart. (2/5206)

Src family kinases are implicated in cellular proliferation and transformation. Terminally differentiated myocytes have lost the ability to proliferate, indicating the existence of a down-regulatory mechanism(s) for these mitogenic kinases. Here we show that feline cardiomyocyte lysate contains thermostable components that inhibit c-Src kinase in vitro. This inhibitory activity, present predominantly in heart tissue, involves two components acting combinatorially. After purification by sequential chromatography, one component was identified by mass and nuclear magnetic resonance spectroscopies as 5'-AMP, while the other was identified by peptide sequencing as a small heat shock protein (sHSP). 5'-AMP and to a lesser extent 5'-ADP inhibit c-Src when combined with either HSP-27 or HSP-32. Other HSPs, including alphaB-crystallin, HSP-70, and HSP-90, did not exhibit this effect. The inhibition, observed preferentially on Src family kinases and independent of the Src tyrosine phosphorylation state, occurs via a direct interaction of the c-Src catalytic domain with the inhibitory components. Our study indicates that sHSPs increase the affinity of 5'-AMP for the c-Src ATP binding site, thereby facilitating the inhibition. In vivo, elevation of ATP levels in the cardiomyocytes results in the tyrosine phosphorylation of cellular proteins including c-Src at the activatory site, and this effect is blocked when the 5'-AMP concentration is raised. Thus, this study reveals a novel role for sHSPs and 5'-AMP in the regulation of Src family kinases, presumably for the maintenance of the terminally differentiated state.  (+info)

Sperm chromatin decondensation by template activating factor I through direct interaction with basic proteins. (3/5206)

Template activating factor I (TAF-I) was originally identified as a host factor required for DNA replication and transcription of adenovirus genome complexed with viral basic proteins. Purified TAF-I was shown to bind to core histones and stimulate transcription from nucleosomal templates. Human TAF-I consists of two acidic proteins, TAF-Ialpha and TAF-Ibeta, which differ from each other only in their amino-terminal regions. Here, we report that TAF-I decondenses demembraned Xenopus sperm chromatin. Human TAF-Ibeta has a chromatin decondensation activity comparable to that of NAP-I, another histone binding protein, whereas TAF-Ialpha has only a weak activity. Analysis of molecular mechanisms underlying the chromatin decondensation by TAF-I revealed that TAF-I interacts directly with sperm basic proteins. Deletion of the TAF-I carboxyl-terminal acidic region abolishes the decondensation activity. Interestingly, the acidic region itself is not sufficient for decondensation, since an amino acid substitution mutant in the dimerization domain of TAF-I which has the intact acidic region does not support chromatin decondensation. We detected the beta form of TAF-I in Xenopus oocytes and eggs by immunoblotting, and the cloning of its cDNA led us to conclude that Xenopus TAF-Ibeta also decondenses sperm chromatin. These results suggest that TAF-I plays a role in remodeling higher-order chromatin structure as well as nucleosomal structure through direct interaction with chromatin basic proteins.  (+info)

Myticin, a novel cysteine-rich antimicrobial peptide isolated from haemocytes and plasma of the mussel Mytilus galloprovincialis. (4/5206)

We report here the isolation of two isoforms of a novel cysteine-rich peptide from haemocytes (isoform A of 4.438 Da and B of 4.562 Da) and plasma (isoform A) of the mussel, Mytilus galloprovincialis. The two molecules display antibacterial activity against gram-positive bacteria, whereas only isoform B is active against the fungus Fusarium oxysporum and a gram-negative bacteria Escherichia coli D31. Complete peptide sequences were determined by a combination of Edman degradation, mass spectrometry and cDNA cloning using a haemocyte cDNA library. The mature molecules, named myticins, comprise 40 residues with four intramolecular disulfide bridges and a cysteine array in the primary structure different to that of the previously characterized cysteine-rich antimicrobial peptides. Sequence analysis of the cloned cDNAs revealed that myticin precursors consist of 96 amino acids with a putative signal peptide of 20 amino acids, the antimicrobial peptide sequence and a 36-residue C-terminal extension. This structure suggests that myticins are synthesized as preproproteins and then processed by various proteolytic events before storage of the active peptide in the haemocytes. Myticin precursors are expressed mainly in the haemocytes as revealed by Northern blot analysis.  (+info)

Subunit organization of the abalone Haliotis tuberculata hemocyanin type 2 (HtH2), and the cDNA sequence encoding its functional units d, e, f, g and h. (5/5206)

We have developed a HPLC procedure to isolate the two different hemocyanin types (HtH1 and HtH2) of the European abalone Haliotis tuberculata. On the basis of limited proteolytic cleavage, two-dimensional immunoelectrophoresis, PAGE, N-terminal protein sequencing and cDNA sequencing, we have identified eight different 40-60-kDa functional units (FUs) in HtH2, termed HtH2-a to HtH2-h, and determined their linear arrangement within the elongated 400-kDa subunit. From a Haliotis cDNA library, we have isolated and sequenced a cDNA clone which encodes the five C-terminal FUs d, e, f, g and h of HtH2. As shown by multiple sequence alignments, defg of HtH2 correspond structurally to defg from Octopus dofleini hemocyanin. HtH2-e is the first FU of a gastropod hemocyanin to be sequenced. The new Haliotis hemocyanin sequences are compared to their counterparts in Octopus, Helix pomatia and HtH1 (from the latter, the sequences of FU-f, FU-g and FU-h have recently been determined) and discussed in relation to the recent 2.3 A X-ray structure of FU-g from Octopus hemocyanin and the 15 A three-dimensional reconstruction of the Megathura crenulata hemocyanin didecamer from electron micrographs. This data allows, for the first time, an insight into the evolution of the two functionally different hemocyanin isoforms found in marine gastropods. It appears that they evolved several hundred million years ago within the Prosobranchia, after separation of the latter from the branch leading to the Pulmonata. Moreover, as a structural explanation for the inefficiency of the type 1 hemocyanin to form multidecamers in vivo, the additional N-glycosylation sites in HtH1 compared to HtH2 are discussed.  (+info)

Isolation, characterization and cDNA cloning of nicotianamine synthase from barley. A key enzyme for iron homeostasis in plants. (6/5206)

Basic cellular processes such as electron transport in photosynthesis and respiration require the precise control of iron homeostasis. To mobilize iron, plants have evolved at least two different strategies. The nonproteinogenous amino acid nicotianamine which is synthesized from three molecules of S-adenosyl-L-methionine, is an essential component of both pathways. This compound is missing in the tomato mutant chloronerva, which exhibits severe defects in the regulation of iron metabolism. We report the purification and partial characterization of the nicotianamine synthase from barley roots as well as the cloning of two corresponding gene sequences. The function of the gene sequence has been verified by overexpression in Escherichia coli. Further confirmation comes from reduction of the nicotianamine content and the exhibition of a chloronerva-like phenotype due to the expression of heterologous antisense constructs in transgenic tobacco plants. The native enzyme with an apparent Mr of approximately 105 000 probably represents a trimer of S-adenosyl-L-methionine-binding subunits. A comparison with the recently cloned chloronerva gene of tomato reveals striking sequence homology, providing support for the suggestion that the destruction of the nicotianamine synthase encoding gene is the molecular basis of the tomato mutation.  (+info)

The phosphotransferase system (PTS) of Streptomyces coelicolor identification and biochemical analysis of a histidine phosphocarrier protein HPr encoded by the gene ptsH. (7/5206)

HPr, the histidine-containing phosphocarrier protein of the bacterial phosphotransferase system (PTS) controls sugar uptake and carbon utilization in low-GC Gram-positive bacteria and in Gram-negative bacteria. We have purified HPr from Streptomyces coelicolor cell extracts. The N-terminal sequence matched the product of an S. coelicolor orf, designated ptsH, sequenced as part of the S. coelicolor genome sequencing project. The ptsH gene appears to form a monocistronic operon. Determination of the evolutionary relationship revealed that S. coelicolor HPr is equally distant to all known HPr and HPr-like proteins. The presumptive phosphorylation site around histidine 15 is perfectly conserved while a second possible phosphorylation site at serine 47 is not well-conserved. HPr was overproduced in Escherichia coli in its native form and as a histidine-tagged fusion protein. Histidine-tagged HPr was purified to homogeneity. HPr was phosphorylated by its own enzyme I (EI) and heterologously phosphorylated by EI of Bacillus subtilis and Staphylococcus aureus, respectively. This phosphoenolpyruvate-dependent phosphorylation was absent in an HPr mutant in which histidine 15 was replaced by alanine. Reconstitution of the fructose-specific PTS demonstrated that HPr could efficiently phosphorylate enzyme IIFructose. HPr-P could also phosphorylate enzyme IIGlucose of B. subtilis, enzyme IILactose of S. aureus, and IIAMannitol of E. coli. ATP-dependent phosphorylation was detected with HPr kinase/phosphatase of B. subtilis. These results present the first identification of a gene of the PTS complement of S. coelicolor, providing the basis to elucidate the role(s) of HPr and the PTS in this class of bacteria.  (+info)

Functional phytohemagglutinin (PHA) and Galanthus nivalis agglutinin (GNA) expressed in Pichia pastoris correct N-terminal processing and secretion of heterologous proteins expressed using the PHA-E signal peptide. (8/5206)

Phytohemagglutinin (Phaseolus vulgaris agglutinin; PHA; E- and L-forms) and snowdrop lectin (Galanthus nivalis agglutinin; GNA) were expressed in Pichia pastoris using native signal peptides, or the Saccharomyces alpha-factor preprosequence, to direct proteins into the secretory pathway. PHA and GNA were present as soluble, functional proteins in culture supernatants when expressed from constructs containing the alpha-factor preprosequence. The recombinant lectins, purified by affinity chromatography, agglutinated rabbit erythrocytes at concentrations similar to the respective native lectins. However, incomplete processing of the signal sequence resulted in PHA-E, PHA-L and GNA with heterogenous N-termini, with the majority of the protein containing N-terminal extensions derived from the alpha-factor prosequence. Polypeptides in which most of the alpha-factor prosequence was present were also glycosylated. Inclusion of Glu-Ala repeats at the C-terminal end of the alpha-factor preprosequence led to efficient processing N-terminal to the Glu-Ala sequence, but inefficient removal of the repeats themselves, resulting in polypeptides with heterogenous N-termini still containing N-terminal extensions. In contrast, PHA expressed with the native signal peptide was secreted, correctly processed, and also fully functional. No expression of GNA from a construct containing the native GNA signal peptide was observed. The PHA-E signal peptide directed correct processing and secretion of both GNA and green fluorescent protein (GFP) when used in expression constructs, and is suggested to have general utility for synthesis of correctly processed proteins in Pichia.  (+info)

Remote homology detection is a hard computational problem. Most approaches have trained computational models by using either full protein sequences or multiple sequence alignments (MSA), including all positions. However, when we deal with proteins in the twilight zone we can observe that only some segments of sequences (motifs) are conserved. We introduce a novel logical representation that allows us to represent physico-chemical properties of sequences, conserved amino acid positions and conserved physico-chemical positions in the MSA. From this, Inductive Logic Programming (ILP) finds the most frequent patterns (motifs) and uses them to train propositional models, such as decision trees and support vector machines (SVM). We use the SCOP database to perform our experiments by evaluating protein recognition within the same superfamily. Our results show that our methodology when using SVM performs significantly better than some of the state of the art methods, and comparable to other. However, our
Experimentally determining the subcellular localization of a protein can be a laborious and time consuming task. Immunolabeling or tagging (such as with a green fluorescent protein) to view localization using fluorescence microscope are often used. A high throughput alternative is to use prediction. Through the development of new approaches in computer science, coupled with an increased dataset of proteins of known localization, computational tools can now provide fast and accurate localization predictions for many organisms. This has resulted in subcellular localization prediction becoming one of the challenges being successfully aided by bioinformatics, and machine learning. Many prediction methods now exceed the accuracy of some high-throughput laboratory methods for the identification of protein subcellular localization.[1] Particularly, some predictors have been developed[2] that can be used to deal with proteins that may simultaneously exist, or move between, two or more different ...
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Applies a random forest algorithm to automatically learn from and then interpret ultraviolet photodissociation (UVPD) mass spectra, passing results to a hidden Markov model for de novo sequence prediction and scoring. We show this combined strategy provides high-performance de novo peptide sequencing, enabling the de novo sequencing of thousands of peptides from an Escherichia coli lysate at high confidence.
TY - JOUR. T1 - NcPred for accurate nuclear protein prediction using n-mer statistics with various classification algorithms. AU - Islam, Md. Saiful. AU - Kabir, Alaol. AU - Sakib, Kazi. AU - Hossain, Alamgir. N1 - 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011) Salamanca, Spain 6-8 April 2011.. PY - 2011. Y1 - 2011. N2 - Prediction of nuclear proteins is one of the major challenges in genome annotation. A method, NcPred is described, for predicting nuclear proteins with higher accuracy exploiting n-mer statistics with different classification algorithms namely Alternating Decision (AD) Tree, Best First (BF) Tree, Random Tree and Adaptive (Ada) Boost. On BaCello dataset [1], NcPred improves about 20% accuracy with Random Tree and about 10% sensitivity with Ada Boost for Animal proteins compared to existing techniques. It also increases the accuracy of Fungal protein prediction by 20% and recall by 4% with AD Tree. In case of Human ...
Extensive study has been conducted on the identification of peptide sequences with mass spectrometry. With the development of computer hardware and algorithms, de novo sequencing has drawn attention from researchers for many years. Because it does not require a protein database, de novo sequencing is able to serve as either a complement of database searching or a stand alone method. As shown by Novor \cite{novor}, the speed of de novo sequencing significantly exceeds the speed of protein database searching. Improving the accuracy of de novo sequencing is essential. Overlapping peptides occur quite frequently in a typical heavy chain proteomics sample. In this thesis, we have proposed an algorithm to efficiently and reliably detect the overlapping peptides. In addition, two strategies named labeling and voting are designed to utilize overlapping peptides so as to improve the accuracy of de novo sequencing. According to the results, the effect of our labeling strategy is not obvious with the ...
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MOTIVATION Peptide-sequencing methods by mass spectrum use the following two approaches: database searching and de novo sequencing. The database-searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. On the other hand, in the case of de novo sequencing, no preliminary information is necessary; however, continuous amino acid sequence peaks and the differentiation of these peaks are required. It is, however, very difficult to obtain and differentiate the peaks of all amino acids by using an actual spectrum. We propose a novel de novo sequencing approach using not only mass-to-charge ratio but also ion peak intensity and amino acid cleavage intensity ratio (CIR). RESULTS Our method compensates for any undetectable amino acid peak intervals by estimating the amino acid set and the probability of peak expression based on amino acid CIR. It provides more accurate identification of sequences than the
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Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly con
SMURFLite (simplified Structural Motifs Using Random Fields) is a web application for protein remote homology detection, specifically in beta-structural proteins.. ::DEVELOPER. Berger Lab. :: SCREENSHOTS. N/A. :: REQUIREMENTS. ...
If you have been following along with the tutorial, by now you have been through several manual de novo sequencing exercises. The one un-blinded, and two blinded sequences have been fairly complete with abundant fragmentation. Just to ground you in reality, this is not always the case, and more often than not the abundance of fragment ions tends to thin near the fringes of the spectrum making it difficult to determine a complete peptide sequence. It also makes it difficult to start a sequence, as your first jump will often be a combination of 2 or 3 amino acids. In addition to this complication, triply charged ions or ions of higher charge states can give fragments of doubly, singly, and triply charge states, making the problem so much more complicated. The de novo problem would seem to lend itself well to a computational solution. Amazingly, until just recently, few if any de novo programs have given satisfactory results leading most experts in the field to say, I can do better by hand. Well, ...
Notice the y ion intensity takes a hit when we encounter glutamic acid, going from y10 to y11 and then again when we cross aspartic acid going from y13 ...
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In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In benchmark suites of protein reference alignments, the core columns of the reference alignment are those that can be confidently labeled as correct, usually due to all residues in the column being sufficiently close in the spatial superposition of the known three-dimensional structures of the proteins. Typically the accuracy of a protein multiple sequence alignment that has been computed for a benchmark is only measured with respect to the core columns of the reference alignment. When computing an alignment in practice, however, a reference alignment is not known, so the coreness of its columns can only be predicted. We develop for the first time a predictor of column coreness for protein multiple sequence alignments. This allows us to predict which columns of a computed alignment are core, and
TY - JOUR. T1 - Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization. AU - Wrabl, James O.. AU - Grishin, Nick V.. PY - 2005/11/15. Y1 - 2005/11/15. N2 - Understanding of amino acid type co-occurrence in trusted multiple sequence alignments is a prerequisite for improved sequence alignment and remote homology detection algorithms. Two objective approaches were used to investigate co-occurrence, both based on variance maximization of the weighted residue frequencies in columns taken from a large alignment database. The first approach discretely grouped amino acid types, and the second approach extracted orthogonal properties of amino acids using principal components analysis. The grouping results corresponded to amino acid physical properties such as side chain hydrophobicity, size, or backbone flexibility, and an optimal arrangement of approximately eight groups was observed. However, interpretation of the orthogonal ...
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.. Register via the University of Cambridge website.. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.. The course involves of a mixture of talks and hands-on exercises.. Day 1 is an ...
Multiple sequence alignments (MSAs) are essential in most bioinformatics analyses that involve comparing homologous sequences. The exact way of computing an optimal alignment between N sequences has a computational complexity of O(LN) for N sequences of length L making it prohibitive for even small numbers of sequences. Most automatic methods are based on the progressive alignment heuristic (Hogeweg and Hesper, 1984), which aligns sequences in larger and larger subalignments, following the branching order in a guide tree. With a complexity of roughly O(N2), this approach can routinely make alignments of a few thousand sequences of moderate length, but it is tough to make alignments much bigger than this. The progressive approach is a greedy algorithm where mistakes made at the initial alignment stages cannot be corrected later. To counteract this effect, the consistency principle was developed (Notredame et al, 2000). This has allowed the production of a new generation of more accurate ...
Download MSAProbs: Multiple Sequence Alignment for free. One of the most accurate multiple protein sequence aligners. MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign.
We reformulate the problem in terms of searching paths in a graph. To this goal, let M P denote the set of ion masses m i in input increased with: their complementary masses m P - m i + 2, the mass of the hydrogen, 1, and of its complementary mass m P - 17. By abuse of notation, M P = {m1,...,m n }, where m i ,m j if i ,j.. We build a directed acyclic graph G P = (V, E) as follows. Let a node v i associate to a member m i of M P , and an edge from v i to v j if m j - m i equals the sum of residue masses.. The de novo sequencing problem consists in determining any path from v1 to v n in the graph G P .. Although there is a unique original protein, the de novo sequencing may have in general more solutions (or none). In order to choose one sequence among the possible solutions, researchers have introduced any scoring function [1-3] depending on the masses of the fragments in the spectra. Our algorithm can determine either the solution of maximum score according to any given function or that of ...
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One way to understand the molecular mechanism of a cell is to understand the function of each protein encoded in its genome. The function of a protein is largely dependent on the three-dimensional structure the protein assumes after folding. Since the determination of three-dimensional structure experimentally is difficult and expensive, an easier and cheaper approach is for one to look at the primary sequence of a protein and to determine its function by classifying the sequence into the corresponding functional family. In this paper, we propose an effective data mining technique for the multi-class protein sequence classification. For experimentations, the proposed technique has been tested with different sets of protein sequences. Experimental results show that it outperforms other existing protein sequence classifiers and can effectively classify proteins into their corresponding functional families ...
One of the core activities of high-throughput proteomics is the identification of peptides from mass spectra. Some peptides can be identified using spectral matching programs like Sequest or Mascot, but many spectra do not produce high quality database matches. De novo peptide sequencing is an approach to determine partial peptide sequences for some of the unidentified spectra. A drawback of de novo peptide sequencing is that it produces a series of ordered and disordered sequence tags and mass tags rather than a complete, non-degenerate peptide amino acid sequence. This incomplete data is difficult to use in conventional search programs such as BLAST or FASTA. DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database. Since the algorithm employed depends on the amino acid composition of the peptide and not its sequence, DeNovoID does not have to consider all possible sequences, but ...
Protein 3D structures, determined largely by their amino acid sequences, have been considered as an essential factor for better understanding the function of proteins [1-3]. However, it is exceedingly difficult to directly predict proteins 3D structures from amino acid sequences [4]. Identifying structure properties, such as secondary structure, solvent accessibility or contact number can provide useful insights into the 3D structures [5-7]. Accurate prediction of structural characteristics from the primary sequence is a crucial intermediate step in protein 3D structure prediction [8, 9].. The solvent accessibility (solvent accessible surface area) is defined as the surface region of a residue that is accessible to a rounded solvent while probing the surface of that residue [10]. Solvent burial residues have a particularly strong association with packed amino acids during the folding process [11], and exposed residues give a useful insight into protein-protein interactions and protein stability ...
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Protein subcellular localization prediction involves the computational prediction of where a protein resides in a cell. It is an important component of bioinformatics-based prediction of protein function and genome annotation, and can also aid us to identify novel drug targets.. Here we use the subcellular localization dataset of human proteins presented in the study of Chou and Shen (2008) for a demonstration. The complete dataset includes 3,134 protein sequences (2,750 different proteins), classified into 14 human subcellular locations. We selected two classes of proteins as our benchmark dataset. Class 1 contains 325 extracell proteins, and class 2 includes 307 mitochondrion proteins.. First, we load the Rcpi package, then read the protein sequences stored in two separated FASTA files with ...
In order to benefit maximally from large scale molecular biology data generated by recent developments, it is important to proceed in an organized manner by developing databases, interfaces, data visualization and data interpretation tools. Protein subcellular localization and microarray gene expression are two of such fields that require immense computational effort before being used as a roadmap for the experimental biologist. Protein subcellular localization is important for elucidating protein function. We developed an automatically updated searchable and downloadable system called model organisms proteome subcellular localization database (MEP2SL) that hosts predicted localizations and known experimental localizations for nine eukaryotes. MEP2SL localizations highly correlated with high throughput localization experiments in yeast and were shown to have superior accuracies when compared with four other localization prediction tools based on two different datasets. Hence, MEP2SL system may ...
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
Multiple sequence alignment for short sequences Kristóf Takács Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of this problem, the research on this topic is focused on aligning…
Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the
Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction ...
The solvent accessibility of a residue in a protein is a value that represents the solvent exposed surface area of this residue. It is crucial for understanding protein structure and function. As a result of the completion of whole-genome sequencing projects, the sequence-structure gap is rapidly increasing. Importantly, the knowledge of protein structures is a foundation for understanding the mechanism of diseases of living organisms and facilitating discovery of new drugs. The most reliable methods for identification of protein structure are X-ray crystallography techniques, but they are expensive and time-consuming. This leads to a central, yet unsolved study of protein structure prediction in bioinformatics, especially for sequences which do not have a significant sequence similarity with known structures [1]. To predict protein structure, the role of solvent accessibility has been extensively investigated as it is related to the spatial arrangement and packing of amino acids during the ...
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Call for Appointment. Contact Information. Rishi Pal Singh (Advocate) Kothi No.2, Ankush (New Courts Chowk), Jalandhar. The mailing address for Dmc is 3990 John R St, , Detroit, Michigan - 48201-2018 (mailing address contact number - 313-993-4136). A proud member of the Detroit Medical Center (DMC), the Childrens Hospital of Michigan is the first childrens hospital in the state. About DMCH. The Heart & Vascular Institute at the DMC has delivered advanced cardiac care to our community for more than three decades. Your review will be posted and available for anyone to read so please keep that in mind when posting personal information. Information on this page is secure. The hospital serves all communities between, Soweto & Vereeniging. By submitting this form you agree to receive periodic health-related information and updates. Phone: 313-993-2507. Fees Payment. 4160 John R. Street Suite 1021 Detroit, MI 48201 (313) 966-9852 (313) 745-8222. Contact Us. 311 Mack Avenue Suite 63100 Detroit, MI ...
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Journal Article: Small-Molecule Transport by CarO, an Abundant Eight-Stranded beta-Barrel Outer Membrane Protein from Acinetobacter Baumannii ...
Title: A Research on Bioinformatics Prediction of Protein Subcellular Localization. VOLUME: 4 ISSUE: 3. Author(s):Gang Fang, Guirong Tao and Shemin Zhang. Affiliation:Department of Life Science, Xian University of Arts and Science, Xian 710065, China.. Keywords:Bioinformatics, prediction, protein subcellular localization, localizome, proteomics, database. Abstract: Protein subcellular localization is one of the key characteristic to understand its biological function. Proteins are transported to specific organelles and suborganelles after they are synthesized. They take part in cell activity and function efficiently when correctly localized. Inaccurate subcellular localization will have great impact on cellular function. Prediction of protein subcellular localization is one of the important areas in protein function research. Now it becomes the hot issue in bioinformatics. In this review paper, the recent progress on bioinformatics research of protein subcellular localization and its prospect ...
The first linear-time suffix tree algorithm was developed by Weiner in 1973. A more space efficient algorithm was produced by McCreight in 1976, and Ukkonen produced an on-line variant of it in 1995. The key to search speed in a suffix tree is that there is a path from the root for each suffix of the text. This means that at most n comparisons are needed to find a pattern of length n. Lloyd Allison has a detailed introduction to suffix trees, which includes a javascript suffix tree demonstration and a discussion of suffix tree applications. His example uses the string mississippi, which can be decomposed into 12 suffixes (Fig 1). A suffix is a substring that includes the final character of the string, for instance the suffix ippi can be found starting at position 8.. A suffix tree can be either implicit (Fig 2a) or explicit (Fig 2b). Suffixes in an implicit suffix tree can end at an interior node -- making them prefixes of another suffix. For example, in the implicit suffix tree for ...
FSA is a probabilistic multiple sequence alignment algorithm which uses a distancebased approach to aligning homologous protein RNA or DNA sequences
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document titled Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques is about AI and Robotics
TY - JOUR. T1 - High performance biological pairwise sequence alignment. T2 - FPGA versus GPU versus cell BE versus GPP. AU - Benkrid, Khaled. AU - Akoglu, Ali. AU - Ling, Cheng. AU - Song, Yang. AU - Liu, Ying. AU - Tian, Xiang. PY - 2012. Y1 - 2012. N2 - This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBMs Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion ...
Hi. Ive been trying to download a multiple sequence alignment from clustal omega as a clustal format file, but whenever I click on the download option, it just opens a new page with only the alignments displayed. I tried downloading the page as a .pdf file and converting it into rtf, but that destroys the formatting. Same thing with simply copy/pasting into a text file. I need a clustal formatted file for use with PriFi ( for designing primers from multiple sequence alignment ). Is there any workaround to this. Or is there something else I can use that does the MSA and the primer design from a multiple sequence fast file. (im using mac os x mavericks ) ...
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
CLUSTAL-W is currently one of the most popular automated multiple sequence alignment tools. CLUSTAL-W calculates a distance matrix for the sequences that are to be aligned. The distance matrix is then used to generate a phylogenetic tree that is used to guide the series of global alignments needed to create the multiple alignment. This is referred to as progressive alignment. Mutliple sequence alignments may also be created by hand and involve gapped or ungapped sequences. Typically, gapped alignments are used for full protein sequences, whereas ungapped alignments may be used to identify protein domains or motifs (See BLOCKS database).. Other multiple sequence alignment methods include DIALIGN, T-Coffee, and POA (Lassman and Sonnhammer, 2002).. ...
The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the ...
Evaluation Measures of Multiple Sequence Alignments - Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of the structure, functionality and, ultimately, the evolution of proteins. A new algorithm, the Circular Sum (CS) method, is presented for formally evaluating the quality of an MSA. It is based on the use of a solution to the Traveling Salesman Problem, which identi es a circular tour through an evolutionary tree connecting the sequences in a protein family. With this approach, the calculation of an evolutionary tree and the errors that it would introduce can be avoided altogether. The algorithm gives an upper bound, the best score that can possibly be achieved by any MSA for a given set of protein sequences. Alternatively, if presented with a speci c MSA, the algorithm provides a formal score for the MSA, which serves as an absolute measure of the quality of the MSA. The CS
CombAlign is a new Python code that generates a gapped, multiple structure-based sequence alignment (MSSA) given a set of pairwise structure-based sequence alignments. CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related structures. The method for combining multiple pairwise alignments is straightforward, involving the recording of pre-computed residue-residue correspondences between positions on the reference protein and each compared structure, and insertion of non-redundant gaps, as needed, to reflect amino-acid deletions or structural divergence in the reference relative to one or more compared structures.. CombAlign is not intended for use in applications for which greater benefit would be provided using a multiple structure alignment as generated by the vast majority of open-source programs [20], nor does it propose to address matters of protein evolution or function ...
This paper presents [email protected], a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.. ...
If histories stem to be diagnosed to exploring download introduction to protein structure prediction: methods and algorithms sources( Kousky et al. 2011, Liao 2012, GFDRR 2012), a easy introduction for complimentary stare support is to draw the ADHD of these variable networks of bias lane, far where able date compendium profiles are proposed. It has usually Maybe the public patternsKnitting of what and where fossil magnitudes re to hijack mandated, but a deeper trial of the controversy cases that look to first vegetation However of the options of being version to growing by large gains. It as is a deeper download introduction to protein structure prediction: methods and of the good personnel and rights of readers monitoring or Cosleeping in the different Archaeology and their low rights for various data.
New prediction server avaliable: Sigfind - Signal Peptide Prediction Server (Human) at http://www.stepc.gr/~synaptic/sigfind.html (C)opyright 2001 by Martin Reczko (martin at stepc.gr) This software (SIGFIND) predicts signal peptides at the start of protein sequences. A novel neural network learning algorithm is used for prediction. It is trained on the human protein data used for the SIGNALP system described in H.Nielsen, J.Engelbrecht, S.Brunak, and G.von Heijne: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Engineering, vol. 10 no. 1 pp. 1-6, 1997 The SIGNALP data is derived from A.Bairoch and B.Boeckmann: The SWISS-PROT protein sequence data bank: current status, Nucleic Acids Res. 22:3578-3580 (1994). Using the same fivefold crossvalidation as SIGNALP, the 5 networks of SIGFIND (avgerage Mathews correlation coefficiant 0.98) perform better than SIGNALP (avgerage Mathews correlation coefficiant 0.96). It should be noted that ...
Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome - Background: Computer programs for the generation of multiple sequence alignments such as Clustal W allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equally conserved, their potential utility as hybridization targets varies. Mismatches in sequence variants are more disruptive in some duplexes than in others. Additionally, the propensity for self-interactions amongst oligonucleotides targeting conserved regions differs and the structure of target regions themselves can also influence hybridization efficiency. There is a need to develop software that will employ thermodynamic selection criteria for finding optimal hybridization targets in related sequences. Results: A new scheme and new software for optimal detection of oligonucleotide hybridization targets common to families of
"NetPhos 2.0 Server". Center for Biological Sequence Analysis. Retrieved 13 May 2013. "SUMOsp 2.0 - SUMOylation Site Prediction ... According to an analysis of the secondary protein structure, TTC39B is most likely to be expressed in the endoplasmic reticulum ... Tetratricopeptide repeat protein 39B is a protein that in humans is encoded by the TTC39B gene. TTC39B is also known as C9orf52 ... "Tetratricopeptide repeat protein 39B isoform 1 [Homo sapiens] - Protein - NCBI". "NCBI". Retrieved 9 May 2013.[permanent dead ...
"Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences. 89 (6 ... Center for Biological Sequence Analysis. Miao, Y.; Cui, L.; Chen, Z.; Zhang, L (2016). "Gene expression profiling of DMU-212- ... Chou, P. Y.; Fasman, G. D. (1978). "Prediction of the secondary structure of proteins from their amino acid sequence". Advances ... Transmembrane Protein 217 is a protein encoded by the gene TMEM217. TMEM217 has been found to have expression correlated with ...
Center of Biological Sequence Analysis. Retrieved 9 May 2015. "NetPhosK 1.0 Server". NetPhosK 1.0 Server. Center of Biological ... Sequence Analysis. Retrieved 9 May 2015. "NetAcet 1.0 Server". NetAcet 1.0 Server. Center of Biological Sequence Analysis. ... Both consists of two exons that include the entire coding sequence for the TMEM251 protein. Figure 1: Chromosome 14 overview. ... Transmembrane protein 251, also known as C14orf109 or UPF0694, is a protein that in humans is encoded by the TMEM251 gene. One ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... Zinc finger protein 226 is a protein that in humans is encoded by the ZNF226 gene. The zinc finger protein 226 is also known as ... sequence and protein-protein interaction information". Nucleic Acids Research. 45 (W1): W291-W299. doi:10.1093/nar/gkx366. PMC ... Analysis to predict post-translational modifications of the protein were conducted on. Based on the results of Expasy's ...
Journal of Protein Sequence and Data Analysis Vol.. 11: 410 - 412 (1993) Characterization of two Platelet Aggregation Inhibitor ... Protein Sequence and Data Analysis. Vol. 15(1): 31 - 32 (1992) Scorpion [Bathus Sindicus] haemocyanin: Primary structure ... He organized six international symposia and workshops on Protein structure function and was a coordinator of the DNA Sequence ... Protein Science Vol 3: 1840-1846 (1994) Cataractous Lens and its Environment. S. Zarina, A. Abbasi and Zafar H. Zaidi. Pure & ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2019-03-03. Sievers F, Wilm A ... Transmembrane protein 179 is a protein that in humans is encoded by the TMEM179 gene. The function of transmembrane protein 179 ... "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the ...
Protein sequence analysis: automated microsequencing. Science. 1983 Feb 11;219(4585):650-9. Brosius J, Dull TJ, Sleeter DD, ... Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... This method was shortly thereafter superseded by automated protein sequencing operating in the low picomole range. From 1977- ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... This protein is also predicted as a DNA binding protein. The protein may assume a tertiary structure of a coiled coil. ... protein name). The mRNA is composed of 6 exons, and encodes a 15007.84 kD protein known as HT021. This protein has a pre- ... Pruitt KD, Tatusova T, Maglott DR (January 2007). "NCBI reference sequences (RefSeq): a curated non-redundant sequence database ...
Combet, C; Blanchet, C; Geourjon, C; Deléage, G (March 2000). "[email protected]: Network Protein Sequence Analysis". Trends in Biochemical ... "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences. 89 (6 ... with several proline-rich sequences (PXXP). Proline-rich domains are usually associated with protein-protein interactions; thus ... Sequence analysis of the SMIM14 gene in humans suggests that the C-terminus encodes a disproportionate amount of proline ...
"Statistical analysis of protein sequence (SAPS)". SDSC Biology Workbench- Protein Tools. Retrieved 4 April 2017. "AAStats". ... "ElDorado: Annotation and Analysis". Genomatix. 2017. "Human genome, search for BEND2 isoform 1 protein". BLAT. "BEN domain ... The presence of nuclear localization signals within the amino acid sequence or primary structure of the BEND2 protein leads to ... The BEND2 protein has 42 known orthologs. The C-terminus of the protein, the location of its BEN domains, is highly conserved; ...
"[email protected]: Network Protein Sequence Analysis - SOPMA". Retrieved 2019-05-05. "I-TASSER server for protein structure and function ... Putative uncharacterized protein C6orf52 (C6orf52) is a protein in humans that is encoded by the gene "C6orf52" and has six ... which are known to alter different functional parameters of proteins such as subcellular localization, protein parenting, DNA ... Two proteins in cattle that have been linked to fat or energy metabolism were predicted to be similar to C6orf52, however there ...
"SAPS, Statistical Analysis of Protein Sequence". SDSC Biology Workbench. "PI, Isoelectric point determination". SDSC Biology ... The KIAA0232 protein is 1395 amino acids in length with a molecular weight of 154.8kDa. It has higher than average frequencies ... "RCSB Protein Data Bank". Archived from the original on 2012-12-27. "NetPhos 2.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-09. ... KIAA0232 is a nuclear phosphoserine protein which in humans is encoded by the KIAA0232 gene. KIAA0232 is located at 4p16.1 ...
The methods for sequence analysis of synthetic polymers differ from the sequence analysis of biopolymers (e. g. DNA or proteins ... Other options besides traditional NMR spectroscopy for sequence analysis are listed here; these include Kerr-effect for ... for the sequence analysis of synthetic copolymers.⁠ NMR spectroscopy allows determination of the relative abundance of ... Structure analysis of the reaction products by IR and 1H and 13C NMR". Journal of Polymer Science: Polymer Physics Edition. 20 ...
"Statistical Analysis of Protein Sequence (Biology Workbench)".[permanent dead link] Meechan DW, Maynard TM, Tucker ES, LaMantia ... Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR, Davis NG (June 2006). "Global analysis of protein ... C22orf25 is also xenologous to T10 like proteins in the Fowlpox Virus and Canarypox Virus. The gene coding for C22orf25 is ... Casey PJ (1995). "Protein lipidation in cell signaling". Science. 268 (5208): 221-5. Bibcode:1995Sci...268..221C. doi:10.1126/ ...
... the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. ... Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2nd ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory ... A DNA sequence is called a "sense" sequence if it is the same as that of a messenger RNA copy that is translated into protein. ... These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. Enzymes can also ...
"Biology Workbench". San Diego Supercomputer Center.[permanent dead link] "SAPS". Statistical Analysis of Protein Sequence, ... The N terminal half of this protein family is a BTB-like domain. BTB domains multifunctional protein-protein interaction motif ... The protein sequence is not rich or low in any amino acids. There are two stretches of non-polar regions, which are capable of ... The protein sequence of KIAA1841 is not rich or low in any amino acids. The same is true in Mus musculus, Danio rerio, ...
"SAPS". Statistical Analysis of Protein Sequence, Biology Workbench.[permanent dead link] "NCBI Structure". The Gene Human ... 2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... FAM83H is a gene in humans that encodes a protein known as FAM83H (uncharacterized protein FAM83H). FAM83H is targeted for the ... Alpha helices comprise the majority of the protein. There is a transmembrane domain from 231-252. Protein FAM83H is targeted to ...
Protein Sequences & Data Analysis. 2 (6): 463-6. PMID 2696959. Atomi H, Ueda M, Hikida M, Hishida T, Teranishi Y, Tanaka A ( ... Only one cysteine residue is conserved between the sequences of the fungal, plant and bacterial enzymes; it is located in the ... Portal: Biology (CS1 maint: uses authors parameter, Protein pages needing a picture, EC 4.1.3, Enzymes of known structure). ... ISBN 978-0-495-10935-8. Cozzone AJ (1998). "Regulation of acetate metabolism by protein phosphorylation in enteric bacteria". ...
Friedberg F, Rhodes C (1988). "Segments of amino acid sequence similarity in beta-amylases". Protein Sequences & Data Analysis ... Three highly conserved sequence regions are found in all known beta-amylases. The first of these regions is located in the N- ... A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different ... Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical ...
Tannu, Nilesh S; Hemby, Scott E (2007). "De novo protein sequence analysis of Macaca mulatta". BMC Genomics. 8: 270. doi: ... Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. In protein ... "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass ... "Probability-based protein identification by searching sequence databases using mass spectrometry data". Electrophoresis. 20 (18 ...
2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY. Pandit ... It is calculated as the average sequence distance between residues that form native contacts in the folded protein divided by ... The contact order of a protein is a measure of the locality of the inter-amino acid contacts in the protein's native state ... Protein structure prediction methods are more accurate in predicting the structures of proteins with low contact orders. This ...
"Statistical Analysis of Protein Sequences". Retrieved 20 April 2014. "Compute pI/Mw tool". Retrieved 10 April 2014. "PSORTII". ... The sequences were retrieved from a BLAST search in humans with the C1orf106 protein. The MSA suggests the proteins share a ... suggests the INAVA protein interacts with 14-3-3 protein sigma, which is an adaptor protein. INAVA is well conserved in ... A multiple sequence alignment (MSA) of potentially paralogous proteins was made to determine the likelihood of a truly ...
"Statistical Analysis of Protein Sequences". EMBL-EBI. 2018. Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and ... C20orf196 has a high protein sequence divergence rate. It is a fast evolving protein. It evolves faster than fibrinogen, as ... protein-protein interaction networks, integrated over the tree of life". Nucleic Acids Research. 43 (Database issue): D447-52. ... RNA-Seq analysis has shown ubiquitous expression of c20orf196 in 26 human tissues: adrenal, appendix, bone marrow, brain, colon ...
As the total number of sequenced proteins increases and interest expands in proteome analysis, an effort is ongoing to organize ... The concept of protein family was conceived at a time when very few protein structures or sequences were known; at that time, ... Dayhoff MO (December 1974). "Computer analysis of protein sequences". Federation Proceedings. 33 (12): 2314-6. PMID 4435228. ... A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family ...
2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. Bibcode:2004Natur.429..369H. doi:10.1038/ ... Analysis of the complement of ribosomal proteins present". J. Biol. Chem. 276 (47): 43958-69. doi:10.1074/jbc.M106510200. PMID ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical ...
2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. Bibcode:2004Natur.429..369H. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... ELAV-like protein 2 is a protein that in humans is encoded by the ELAVL2 gene. GRCm38: Ensembl release 89: ENSMUSG00000008489 ... Gao FB, Keene JD (1997). "Hel-N1/Hel-N2 proteins are bound to poly(A)+ mRNA in granular RNP structures and are implicated in ...
Physicochemical characterization, cloning, sequence analysis, and heterologous gene expression". The Journal of Biological ... methyl-Co(III)+methylamine-specific+corrinoid+protein):coenzyme+M+methyltransferase at the US National Library of Medicine ... This enzyme catalyses the following chemical reaction [methyl-Co(III) methylamine-specific corrinoid protein] + coenzyme M ⇌ ... Methyl-Co(III) methylamine-specific corrinoid protein):coenzyme M methyltransferase (EC, methyltransferase 2, MT2, ...
Physicochemical characterization, cloning, sequence analysis, and heterologous gene expression". The Journal of Biological ... methanol-specific corrinoid protein] Free methylcob(I)alamin can substitute for the corrinoid protein in vitro. LeClerc GM, ... Cloning, sequencing and differential transcription of the encoding genes, and functional overexpression of the mtaA gene in ... methyl-Co(III)+methanol-specific+corrinoid+protein):coenzyme+M+methyltransferase at the US National Library of Medicine Medical ...
Brenner, S. E.; Koehl, P.; Levitt, M. (2000). "The ASTRAL compendium for protein structure and sequence analysis". Nucleic ... Gerstein, M.; Levitt, M. (1997). "A structural census of the current population of protein sequences". PNAS. 94 (22): 11911- ... Michael Levitt publications indexed by Google Scholar Levitt, Michael (1972). Conformation analysis of proteins (PhD thesis). ... Levitt, M. (1976). "A simplified representation of protein conformations for rapid simulation of protein folding". Journal of ...
2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. Bibcode:2004Natur.429..369H. doi:10.1038/ ... The protein belongs to the L29P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ... 2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proceedings of the ... 60S ribosomal protein L35 is a protein that in humans is encoded by the RPL35 gene. Ribosomes, the organelles that catalyze ...
2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. Bibcode:2001Natur.414.. ... 2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
"A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ... Transition state analyses have used isotopic effects and quantum calculations to reveal a completely dissociated dianionic ... Suttle DP, Bugg BY, Winkler JK, Kanalas JJ (Mar 1988). "Molecular cloning and nucleotide sequence for the complete coding ... It is believed that the two separate catalytic sites fused into a single protein to stabilize its monomeric form. The covalent ...
Directed evolution protein-protein interactions PelB leader sequence Competing techniques: Two-hybrid system mRNA display ... While pVI has been useful for the analysis of cDNA libraries, pIII and pVIII remain the most utilized coat proteins for phage ... Phage display is a laboratory technique for the study of protein-protein, protein-peptide, and protein-DNA interactions that ... Target proteins or DNA sequences are immobilized to the wells of a microtiter plate. Many genetic sequences are expressed in a ...
PTGS-2 is a sequence homodimer. Each monomer of the enzyme has a peroxidase and a PTGS (COX) active site. The PTGS (COX) ... Picot D, Loll PJ, Garavito RM (January 1994). "The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1 ... Xiao G, Tsai AL, Palmer G, Boyar WC, Marshall PJ, Kulmacz RJ (February 1997). "Analysis of hydroperoxide-induced tyrosyl ... Dong L, Vecchio AJ, Sharma NP, Jurban BJ, Malkowski MG, Smith WL (May 2011). "Human cyclooxygenase-2 is a sequence homodimer ...
The authors' analysis of the strains showed that many carried blaNDM-1 on plasmids, which will allow the gene to be readily ... Protein pages needing a picture, Articles containing potentially dated statements from June 2010, All articles containing ... and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from ...
... a major structural protein (VP1) of about 58~60 kDa and a minor capsid protein (VP2). The most variable region of the viral ... The cloning and sequencing of the Norwalk virus genome showed that these viruses have a genomic organization consistent with ... Nguyen GT, Phan K, Teng I, Pu J, Watanabe T (October 2017). "A systematic review and meta-analysis of the prevalence of ... The protein MDA-5 may be the primary immune sensor that detects the presence of noroviruses in the body. Some people have ...
... has been shown to interact with SKI protein and it is also known to interact with AP-1. NFI-X3 has been shown to interact ... Norquay LD, Yang X, Sheppard P, Gregoire S, Dodd JG, Reith W, Cattini PA (2003). "RFX1 and NF-1 associate with P sequences of ... Apt D, Liu Y, Bernard HU (1994). "Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference ... Nuclear factor 1 X-type is a protein that in humans is encoded by the NFIX gene. NFI-X3, a splice variant of NFIX, regulates ...
From an analysis of the PANO1 protein, it was observed that the protein contains a low amount of lysine and a very low amount ... "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-08-01. "PSORT II Prediction". psort.hgc.jp. Retrieved ... "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2021-08-01. (CS1 maint: url- ... Stimulating protein 1, CCAAT/enhancer binding protein, GC box elements and HMG box-containing protein 1. Like previously ...
2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Homeobox protein Hox-D8 is a protein that in humans is encoded by the HOXD8 gene. This gene belongs to the homeobox family of ... HOXD8+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from ... 1989). "Complementary homeo protein gradients in developing limb buds". Genes Dev. 3 (5): 641-50. doi:10.1101/gad.3.5.641. PMID ...
... "c-Src protein expression is increased in human breast cancer. An immunohistochemical and biochemical analysis". J. Pathol. 180 ... Both the N-terminally attached myristic acid and the peptide sequences of the unique region are involved in the interaction. ... c-Src can be activated by many transmembrane proteins that include: adhesion receptors, receptor tyrosine kinases, G-protein ... Proto-oncogene tyrosine-protein kinase Src, also known as proto-oncogene c-Src, or simply c-Src (cellular Src; pronounced "sarc ...
Durbin, Richard (23 April 1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge ... An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ ... This is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 ... Feature analysis is first undertaken on temporal and/or spectral features of the speech signal. This produces an observation ...
The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (3): 197-205. doi: ... 2005). "The sequence and analysis of duplication-rich human chromosome 16". Nature. 432 (7020): 988-94. Bibcode:2004Natur.432.. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... C-jun-amino-terminal kinase-interacting protein 3 is an enzyme that in humans is encoded by the MAPK8IP3 gene. The protein ...
Multiple EM for Motif Elicitation Nucleic acid sequence Protein primary structure Protein I-sites Sequence logo Sequence mining ... researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. Such techniques belong ... a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be ... When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical ...
The syndrome is caused by mutations in both copies of the CENPF gene, which codes for centromere protein F. This protein is ... Methods of genetic detection include whole exome sequencing and panel testing, which involves sequencing a selection of ... conducted a genetic analysis on a British family in which four foetuses had miscarried with symptoms of a ciliopathy. They ... CENPF codes for centromere protein F. Centromere proteins are involved in the separation of chromosomes during cell division. ...
... providing an understanding of how proteins may function in high salinity and low water activity conditions. The genome sequence ... the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence ... In the 1990s, he organized and led the team that deciphered the first genome sequence and genetic code for a halophilic microbe ... Post-genomic research in his laboratory established the core and signature proteins in halophilic Archaea, and the function of ...
Blood sample DNA sequencing of the 26S ribosomal subunit can definitively identify C. blankii. In nature, Candida blankii forms ... Candida blankii was discovered in the 1960s, after the analysis of the organs of infected mink in Canada by F. Blank. These ... A diploid isolate of C. blankii had an observed "potential for use in single cell protein production from hemicellulose ...
"Sequence analysis of a mannitol dehydrogenase cDNA from plants reveals a function for the pathogenesis-related protein ELI3". ...
2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Epidermal growth factor receptor kinase substrate 8-like protein 1 is an enzyme that in humans is encoded by the EPS8L1 gene. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Tocchetti A, Confalonieri S, Scita G, Di Fiore PP, Betsholtz C (Mar 2003). "In silico analysis of the EPS8 gene family: genomic ...
Palme K, Hesse T, Campos N, Garbers C, Yanofsky MF, Schell J (February 1992). "Molecular analysis of an auxin binding protein ... represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ... In molecular biology, the auxin binding protein family is a family of proteins which bind auxin. They are located in the lumen ... The primary structure of these proteins contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could ...
V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1". DNA ... 2004). "Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode: ...
The primary structure, or amino acid sequence identity, of the proteins between paralogs is ~60% identical and between ... PCR analysis identified the homozygous null mutation to be in the ODZ3 gene, which is important for the early developing eye. ... "Teneurin proteins possess a carboxy terminal sequence with neuromodulatory activity". Molecular Brain Research. 133 (2): 253-65 ... The proteins were called Ten-ms in zebrafish, teneurins in chicken, Ten-m1-4, Odz1-4, Ten-m/Odz1-4, DOC4 in mouse, neurestin in ...
To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point of H. ... Whole genome sequences are available for two strains of H. salinarum, NRC-1 and R1. The Halobacterium sp. NRC-1 genome consists ... Vreeland, H; Rosenzweig, W D; Lowenstein, T; Satterfield, C; Ventosa, A (December 2006). "Fatty acid and DNA analyses of ... salinarum proteins is 5.03. These highly acidic proteins are overwhelmingly negative in charge and are able to remain in ...
Protein Science. 13 (10): 2819-24. doi:10.1110/ps.04682504. PMC 2286551. PMID 15340161. LILRA3+protein,+human at the US ... Norman PJ, Carey BS, Stephens HA, Vaughan RW (June 2003). "DNA sequence variation and molecular genotyping of natural killer ... Zhang Z, Henzel WJ (October 2004). "Signal peptide prediction based on analysis of experimentally verified cleavage sites". ... is a protein that in humans is encoded by the LILRA3 gene located within the leukocyte receptor complex on chromosome 19q13.4. ...
The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 6 (1): 63-70. ... "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nature Biotechnology ... Cordon-bleu protein-like 1 is a protein that in humans is encoded by the COBLL1 gene. GRCh38: Ensembl release 89: ... "Prediction of the coding sequences of unidentified human genes. XIII. ...
Amino acids are made into proteins by being joined in a chain of peptide bonds. Each different protein has a unique sequence of ... Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R (November 1996). "Complete sequence analysis of the genome of ... amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have ... These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites ...
2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2001). "Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing". EMBO Rep. 1 (3): 287- ... WD repeat domain phosphoinositide-interacting protein 2 is a protein that in humans is encoded by the WIPI2 gene. WD40 repeat ...
"DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic ... Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C (August 2010). "High-resolution analysis of parent-of-origin ... ISBN 0-470-02262-0. Wolf JB, Cheverud JM, Roseman C, Hager R (June 2008). "Genome-wide analysis reveals a complex pattern of ... Lazaraviciute G, Kauser M, Bhattacharya S, Haggarty P, Bhattacharya S (2014). "A systematic review and meta-analysis of DNA ...
January 2003). "Sequence analysis of the granulysin and granzyme B genes in familial hemophagocytic lymphohistiocytosis". Human ... It exists in its own granule after translation, and release of the protein is triggered by Protein Kinase C (PKC). Its C- and N ... It is expressed in 2 forms: a 15kDa precursor protein, the translation product, and a 9kDa cytotoxic protein, which is formed ... Orthologs of this protein are found in most mammal species, such as in cows and pigs, however not in rodents. Granulysin is ...
The transcriptome of E. gracilis was recently sequenced, providing information about all of the genes that the organism is ... although a later molecular analysis showed that E. gracilis was, in fact, more closely related to Astasia longa than to certain ... Evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the ...
Wernegreen, J. J.; Moran, N. A. (1999-01-01). "Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein- ... The loss of large section of genomes could in fact lead to a loss in promotor sequences. This could in fact pushed the ... the microsporidia shrunk its genome eliminating almost 1000 genes and reduced even the size of protein and protein-coding genes ... Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the ...
Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids. Biological Sequence Analysis Probabilistic ... Durbin, Richard is the author of Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids, published ... Models of Proteins and Nucleic Acids. by Durbin, Richard, Eddy, Sean R., Krogh, Anders S. by Durbin, Richard, Eddy, Sean R., ...
Protein structure prediction ... – A free PowerPoint PPT presentation (displayed as an HTML5 slide show) on PowerShow.com ... Amino-acids of two sequences can be aligned and we can easily count the number ... Check pairwise alignment. ... Protein sequence analysis allows protein classification 6. Development of protein sequence databases*Atlas of protein sequence ... Protein Sequence Analysis - Overview - - ... and protein bioinformatics (protein sequence ... Protein Bioinformatics. Mixture ...
... and Edman sequencing. Forty-six large subunit proteins were found, 22 of which showed masses in accordance with the SwissProt ... For nine proteins (L3, L4, L5, L7A, L10, L14, L19, L31, and L40), the molecular masses could not be determined. Proteins P1 and ... The 60S ribosomal proteins were isolated from ribosomes of human placenta and separated by reversed phase HPLC. The fractions ... A loss of methionine without acetylation was found for protein L8 and L17. ...
... cDNA cloning and sequence analysis of a pathogen-induced thaumatin-like protein from rice (Oryza sativa). Plant Physiology 101( ... Molecular cloning and sequence analysis of cytoplasmic ribosomal protein gene OsRPS7 from rice (Oryza sativa L.). Hereditas ... A rice (Oryza sativa L.) cDNA encodes a protein sequence homologous to the eukaryotic ribosomal 5S RNA-binding protein. Plant ... cDNA cloning and sequence analysis of a pathogen-induced traumatin-like protein from rice (Oryza sativa). cDNA cloning and ...
BRAF/KRAS gene sequencing of sebaceous neoplasms after mismatch repair protein analysis. Hum Pathol. 2014 Jun; 45(6):1213-20. ... BRAF/KRAS gene sequencing of sebaceous neoplasms after mismatch repair protein analysis. ... BRAF/KRAS gene sequencing of sebaceous neoplasms after mismatch repair protein analysis. ...
Sequence Analysis, Protein. Abstract. ,p,Statistical analysis of alignments of large numbers of protein sequences has revealed ... Revealing evolutionary constraints on proteins through sequence analysis.. Title. Revealing evolutionary constraints on ... Algorithms, Amino Acid Sequence, Animals, Computational Biology, Evolution, Molecular, Models, Molecular, Proteins, Rats, ... Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to ...
... motility mutant pf-14 fails to assemble radial spokes because of a deficiency for assembly-competent radial spoke protein 3 ... Molecular cloning and sequence analysis of the Chlamydomonas gene coding for radial spoke protein 3: flagellar mutation pf-14 ... the sequence similarities between intervening sequences of the radial spoke protein 3 gene and a conserved intervening sequence ... Molecular cloning and sequence analysis of the Chlamydomonas gene coding for radial spoke protein 3: flagellar mutation pf-14 ...
Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 ... Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties ... Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 ... Whole-genome sequence analysis and homology modelling of the main protease and non-structural protein 3 of SARS-CoV-2 reveal an ...
Cloning and sequence analysis of genomic fragment encoding 190KD protein antigen of HL-93 spotted fever group Rickettsiae. In: ... Cloning and sequence analysis of genomic fragment encoding 190KD protein antigen of HL-93 spotted fever group Rickettsiae. / ... Cloning and sequence analysis of genomic fragment encoding 190KD protein antigen of HL-93 spotted fever group Rickettsiae. ... Zhang J, Fan M, Bi D. Cloning and sequence analysis of genomic fragment encoding 190KD protein antigen of HL-93 spotted fever ...
Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications or Mol Biol ... Comparative analysis of dynamics of drug target proteins and model systems from experiments (PCA) and theory (ANM). See the ... Comparative analysis of p38 MAP kinase dynamics from experiments (PCA), simulations (EDA), and theory (ANM). See the Protein ... SignDy: Discovering the Signature Dynamics of Protein Families with Elastic Network Model Analysis. Mol Biol Evol 2019 36(9): ...
Protein Binding * Regulatory Elements, Transcriptional / genetics* * Sequence Analysis, DNA / methods* * Software* * ... For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological ... In silico detection of sequence variations modifying transcriptional regulation PLoS Comput Biol. 2008 Jan;4(1):e5. doi: ... Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach ...
The poplar rust-induced secreted protein (RISP) is a small cationic protein of unknown function that was identified as the most ... The poplar Rust-Induced Secreted Protein (RISP) is a small cationic protein of unknown function that was identified as the most ... Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses. ... Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses. ...
Using sequence and structural analyses, we show that 21% of titins I-band Ig domains contain a conserved cysteine triad that ... Analysis of Ig sequences and structures. The 151 sequences of Ig domains are automatically annotated in the canonical titin ( ... D.G. produced proteins. D.G. and K.Y. did AFM experiments, structural and bioinformatic analyses. D.G. programmed Monte Carlo ... Using sequence and structural analyses, we show that 21% of titins I-band Ig domains contain a conserved cysteine triad that ...
T1 - Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c, a unique protein with a ... Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c, a unique protein with a ... Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c, a unique protein with a ... title = "Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c, a unique protein with ...
A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the ... Phylogenetic analysis showed the single-domain FKBPs to evolve prior to the multi-domain FKBPs, whereas the multi-domain ... class of proteins is present in all known eukaryotes, prokaryotes, and archaea, and it is comprised of three member families ... protein vs. protein) and TBLASTN (protein against DNA sequence) searches [146] on all genomes except for that of R. oryzae, ...
Isolation and DNA sequence analysis of distantly related fatty acid and retionol binding protein gene of Setaria digitata. ... was completely sequenced by PCR cycle sequencing. The sequence showed (64 percent) AT richness. When this sequence was aligned ... YATAWARA, MDMLDK, Isolation and DNA sequence analysis of distantly related fatty acid and retionol binding protein gene of ... of homology to Brugia malayi FAR protein gene sequence. Amino acid sequence deduced from this region (36 amino acids) had 100 ...
Home/Posts/Events 2017/Enabling global analysis of protein expression by next generation sequencing ... Enabling global analysis of protein expression by next generation sequencing. June 7, 2017 ... of protein families and nucleic acid sequences and has developed new methods for gene identification and for the analysis of ... by which protein expression can be monitored and discovered with high coverage and resolution by deep-sequencing the ...
A Proteos Program Retrospective: Establishing Protein Sequencing for Forensic Analysis. Thursday September 16th, 2021 // 9:30 ... Home // Event // A Proteos Program Retrospective: Establishing Protein Sequencing for Forensic Analysis ... For protein sequencing, we have utilized both targeted and non-targeted protein detection using nanoflow liquid chromatography- ... This protein fraction can then be stored frozen and considered for analysis only if a sample did not produce a DNA profile ...
Analysis of worldwide sequence mutations in Zika virus proteins E, NS1, NS3 and NS5 from a structural point of view. ... Moreover, the structural analysis of ZIKV proteins, together with the mutational landscape of ZIKV and a structure-sequence ... Analysis of worldwide sequence mutations in Zika virus proteins E, NS1, NS3 and NS5 from a ... We present here an analysis of all ZIKV sequences available in Genbank up to April 2016, studying the mutations in the whole ...
Nucleotide sequence of regions homologous tonifH (nitrogenase Fe protein) from the nitrogen-fixing archaebacteriaMethanococcus ... 59 BASIC BIOLOGICAL SCIENCES; bioinformatics; metagenomics; next-generation sequencing; nitrogen fixation; sequence analysis; ... easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this ... easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this ...
Protein Interactions & Molecular Networks (protein interactions). Protein Structure & Function. Sequence Analysis (proteins). ... Sequence Analysis (genes). *Proteins:. Evolution and Comparative Genomics (proteins). ... Protein Interactions & Molecular Networks. Natasa Przulj, Hidde de Jong. Protein Structure & Function. Lenore Cowen, Jianlin ... Protein Interactions & Molecular Networks (molecular networks). Submitters will choose the track area best suited to their ...
Analysis of virus mutants, virus populations, and their cell biology allowed us to identify a short-ordered stretch of amino ... Virus mutants deficient in this feature generate compensatory mutations by duplication of their own sequence that restore the ... The C-terminal ~200 amino acids of the PLRV RTP are characteristically disordered yet this protein domain is involved in virus ... Author summary Protein function is often dependent on its structure that is determined by the composition and chemistry of its ...
DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article ... cilia- and flagella-associated protein 95; protein CFAP95. Names. protein C9orf135. uncharacterized protein C9orf135. ... mRNA and Protein(s) * NM_001010940.3 → NP_001010940.1 cilia- and flagella-associated protein 95 isoform 1 ... These reference sequences exist independently of genome builds. Explain. These reference sequences are curated independently of ...
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic ... BIN1 protein, human. GBA protein, human. glucosylceramidase. nuclear protein. signal transducing adaptor protein. SNCA protein ... gene sequence. genetic risk score. genetic susceptibility. genome analysis. genome-wide association study. human. Parkinson ... Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic ...
Background In epigenetic analysis, both the increasing ease of high-throughput sequencing. June 30, 2019. rawveronica0 comments ... Background In epigenetic analysis, both the increasing ease of high-throughput sequencing and a greater desire for genome-wide ... Background In epigenetic analysis, both the increasing ease of high-throughput sequencing. Home / Uncategorized / Background In ... This analysis identified bona fide active promoters (utility, we further investigated whether factors that are specifically ...
  • Proteomic LC-MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re-annotation of the ribosomal protein genes. (semanticscholar.org)
  • The unphosphorylated isoform of radial spoke protein 3 is identified, and the sequence similarities between intervening sequences of the radial spoke protein 3 gene and a conserved intervening sequence of the two Chlamydomonas beta-tubulin genes (Youngblom, J., J. A. Schloss, and C. D. Silflow. (rupress.org)
  • For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. (nih.gov)
  • Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana. (ncsu.edu)
  • To identify genes and miRNAs involved in drought stress responses in S. tonkinensis , both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. (biomedcentral.com)
  • accordingly, many proteins are ignored by the currently available databases of cognate proteins, despite the high amount of important genes that are functionally described only for these incomplete proteomes. (uni.lu)
  • All symbols represent proteins coded by genes known to be involved in HSCR or novel genes identified in this study. (biomedcentral.com)
  • In addition, over the past 4 years, the NIH funded Centers for Mendelian Genomics have conducted sequencing and analysis of protein-coding portions of more than 20,000 human genomes and have identified over 740 genes that likely cause genetic diseases. (cdc.gov)
  • 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)
  • Our goal was to obtain tag sequences from the maximum number of possible genes and to deposit them in the publicly accessible database for ESTs (dbEST of the National Center for Biotechnology Information). (elsevier.com)
  • The EST sequencing data analysis showed 60 novel genes found only in this cDNA library after BLAST analysis against 3.0 million ESTs in NCBI's dbEST database. (elsevier.com)
  • Analyses of targets of the induced microRNAs, from the different libraries, revealed that these molecules may potentially regulate in the cell wall, by repressing genes involved in the synthesis and degradation of glucans and chitin. (figshare.com)
  • Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. (cgrb.org)
  • MADS-box genes encode proteins that share a highly conservative DNA-binding domain, the MADS domain, which recognizes similar 10-bp A/T-rich DNA sequences, the CArG-box [ 4 ]. (biomedcentral.com)
  • In plants, MADS-box genes can be divided into two distinct groups, namely type I and type II lineages: type I MADS-box proteins have no keratin-like (K) domain and only have the MADS (M) domain, whereas type II proteins also possess an intervening (I) domain, a K domain, and a C-terminal region followed by an M domain [ 15 ]. (biomedcentral.com)
  • Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. (upf.edu)
  • Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report. (jax.org)
  • It is speculated that they may respond to multiple fungal signals, and play an important role in potato's broad-spectrum resistance to fungal diseases, and can be used as candidate genes for further needed on disease resistance and functional analysis. (chinacrops.org)
  • Subsequent genomic sequence analysis of multiple genes including elongation factor 3, a component of fungi protein synthesis not found in protozoa, further supported this notion. (medscape.com)
  • Histological and immunohistochemical evaluation, and a next generation sequencing assay (Oncopanel, Illumina, 500 genes) including breaKmer analysis for chromosomal rearrangements were performed. (vdocuments.mx)
  • The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. (elsevier.com)
  • In familial pituitary adenoma patients it is common that no germline defects are found after screening of aryl hydrocarbon receptor interacting protein (AIP) and other genes known to underlie the condition, suggesting the existence of yet unknown predisposition genes. (ox.ac.uk)
  • We do this by getting a DNA sample from you, sequencing most or all of your genes, and comparing that to what we know about your personal and family health histories. (genome.gov)
  • Managed by the Broad Institute of MIT and Harvard, the browser gives access to results from analyses of whole exome sequencing data from 300,000 UK Biobank phenotypes to identify associations between distinct genes or genetic http://journeyman.online/buy-cheap-avalide-online variants and disease. (antiwaft.com)
  • More broadly, the methods developed during this study may provide an important tool for the analysis of whole genome sequencing data aimed at uncovering genes for other genetic diseases. (who.int)
  • and major capsid protein and minor capsid protein genes, complete cds. (cdc.gov)
  • In silico digestion of all 409 ribosomal protein sequences in Arabidopsis defined the proportion of theoretical gene-specific peptides for each gene family and highlighted the need for low m/z cutoffs of MS ion selection for MS/MS to characterize low molecular weight, highly basic ribosome proteins. (semanticscholar.org)
  • BRAF/KRAS gene sequencing of sebaceous neoplasms after mismatch repair protein analysis. (umassmed.edu)
  • Molecular cloning and sequence analysis of the Chlamydomonas gene coding for radial spoke protein 3: flagellar mutation pf-14 is an ochre allele. (rupress.org)
  • Here, we raise an antiserum to protein 3 and use it to isolate the corresponding structural gene from an expression library. (rupress.org)
  • Southern blot analysis indicates that the gene is single copy and has not undergone major rearrangement in mutant pf-14 cells. (rupress.org)
  • However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. (nih.gov)
  • The poplar rust-induced secreted protein (RISP) is a small cationic protein of unknown function that was identified as the most induced gene in poplar leaves during immune responses to the leaf rust pathogen Melampsora larici-populina , an obligate biotrophic parasite. (frontiersin.org)
  • A 3.5-kb DNA fragment, containing the gene encoding cytochrome c'' (cycA), has been cloned and sequenced. (unl.pt)
  • The cytochrome c'' gene codes for a pre-protein with a typical prokaryotic 20-residue signal sequence, suggesting that the protein is synthesised as a precursor which is processed during its secretion into the periplasm. (unl.pt)
  • He is the author of extensive work on properties and evolution of protein families and nucleic acid sequences and has developed new methods for gene identification and for the analysis of sequencing data. (mbcbiolabs.com)
  • Expression of a plant gene with sequence similarity to animal TGF-beta receptor interacting protein is regulated by brassinosteroids and required for normal plant development. (ncsu.edu)
  • Bioinformatic analysis of marker gene sequences also requires considerable expertise. (osti.gov)
  • The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. (osti.gov)
  • Creation of genome-wide protein expression libraries using random activation of gene expression. (nih.gov)
  • The gene for one abundant surface protein was cloned and analyzed. (usda.gov)
  • The gene encoding the abundant, surface exposed 23 kDa protein was identified by screening a B. pilosicoli 95-1000 genome library with the MAb and was expressed in Escherichia coli. (usda.gov)
  • Analyses of the partial sequence of TIG1 suggest that it represents a novel gene product. (cdc.gov)
  • Furthermore, these analyses demonstrate that the transcription activation functions of both AhR and Amt are required for the induction of the gene. (cdc.gov)
  • In the present study a quantitative comparison of amino acid sequence from envelope-nonstructural protein 1 gene junction region of 10 dengue virus type 2 (DEN-2) isolates from Delhi with 12 DEN-2 isolates from diverse geographical areas and hosts provided sufficient information for estimating genetic relationships. (who.int)
  • Throughout her life, she has received a number of medical opinions but it wasn't until she was in her forties, that she received a definitive diagnosis using exome sequencing that confirmed that a particular gene mutation was responsible for her condition. (cdc.gov)
  • C (p.Leu439Pro) of the MTHFR gene in the first three fetuses were found by whole-exome sequencing. (biomedcentral.com)
  • To determine the likely pathogenic gene variants in the family pedigree, we performed whole-exome sequencing in this study. (biomedcentral.com)
  • Genomic analysis revealed several unique amino acid substitutions among the polyprotein gene. (cdc.gov)
  • The TTN gene provides instructions for making a very large protein called titin. (medlineplus.gov)
  • It is unclear how TTN gene variants cause centronuclear myopathy, but it is likely that a shortage of normal titin protein leads to dysfunction of the sarcomere. (medlineplus.gov)
  • These genetic changes occur near the end of the TTN gene and lead to the production of an abnormally short version of the titin protein. (medlineplus.gov)
  • Comparisons of our EST sequencing data with nonredundant human mRNA and protein databases showed that the ESTs represent 1860 gene clusters. (elsevier.com)
  • The gene expression profile of this cell type is revealed by analyzing both the frequency with which a message is encountered and the functional categorization of expressed sequences. (elsevier.com)
  • Comparing an EST sequence with the human genomic sequence database enables assignment of an EST to a specific chromosomal region (a process called digital gene localization) and often enables immediate partial determination of intron/exon boundaries within the genomic structure. (elsevier.com)
  • It is expected that high-throughput EST sequencing and data mining analysis will greatly promote our understanding of gene expression in these cells and of growth and development of the skeleton. (elsevier.com)
  • Association of IL-27 gene rs153109 and rs17855750 polymorphisms with preeclampsia susceptibility and severity: Meta-analysis and trial sequential analysis. (cdc.gov)
  • The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene. (plos.org)
  • Belted mice have sequence variants in the Adamts20 gene encoding a secreted metalloprotease [ 16 ], which was shown to be required for melanoblast survival [ 17 ]. (plos.org)
  • Independently, a gene-based case-control association study was conducted via an exome sequencing dataset of 18 phenotypically similar case subjects and 1,917 control subjects. (ox.ac.uk)
  • BACKGROUND: Individuals with exceptional longevity and their offspring have significantly larger high-density lipoprotein concentrations (HDL-C) particle sizes due to the increased homozygosity for the I405V variant in the cholesteryl ester transfer protein (CETP) gene. (eur.nl)
  • We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. (elsevier.com)
  • Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. (elsevier.com)
  • Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. (elsevier.com)
  • 7 Primers designed to amplify the partial groEL gene encoding heat-shock protein of Anaplasma phagocytophilum EphplgroELF (5′-ATGGTATGCAGTTTGATCGC-3′) and EphplgroELR (5′-TCTACTCTGTCTTTGCGTTC-3′) were used and expected to yield a 625-bp product for Anaplasma phagocytophilum and for Anaplasma platys , respectively. (who.int)
  • The study analysed the evolutionary history of ATM by comparing the gene in various vertebrate and invertebrate species to determine which components were crucial to ATM protein function. (who.int)
  • Complete genomic and cDNA nucleotide sequences were determined, and the pf-14 mutation was identified. (rupress.org)
  • Genomic fragment encoding 190kD protein antigen was amplified from spotted fever group (SFG) rickettsiae HL-93 strain by polymerase chain reaction with a pair of primers Rr 190. (utmb.edu)
  • 602n which were designed from DNA sequences encoding 190kD protein antigen of R. rickettsii and cloned into E. coli JM101 by using plasmid vector PGEM-T. The genomic fragment was sequenced and compared with that of R. rickettsii and R. japonica which were reported previously. (utmb.edu)
  • Zhang, J, Fan, M & Bi, D 1996, ' Cloning and sequence analysis of genomic fragment encoding 190KD protein antigen of HL-93 spotted fever group Rickettsiae ', Chinese Journal of Microbiology and Immunology , vol. 16, no. 3, pp. 227-230. (utmb.edu)
  • CHAPTER 1: Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. (elsevier.com)
  • CHAPTER 4: Features of protein-protein interactions in two-component signaling deduced from genomic libraries. (elsevier.com)
  • Read our application note to learn more about how BioLegend's antibodies were used with the Mission Bio Tapestri platform to reveal novel correlations between genomic variants and protein expression in AML samples. (biolegend.com)
  • Here, we present Sequencing Annotation and Visualization of RNA structures (SAVoR), a web server, which seamlessly links RNA structure predictions with sequencing data and genomic annotations to produce highly informative and annotated models of RNA secondary structure. (upenn.edu)
  • Amino-acids of two sequences can be aligned and we can easily count the number of identical residues (or use an index of similarity) as a measure of relatedness. (powershow.com)
  • Using sequence similarity analyses, these authors proposed that 40% of the I-band Ig domains contain cysteines at positions that form the classical disulfide bond connecting β-strands B and F in extracellular Ig domains such as antibodies. (nature.com)
  • Immediately downstream from cytochrome c'' a second open reading frame (ORF) codes for a 23-kDa protein with similarity to the cytochrome b-type subunit of Ni-Fe hydrogenase. (unl.pt)
  • As we introduce the formalism, we develop a worked example, concerning the analysis of similarity among chemical elements regarding their ability to combine into binary compounds. (benthamscience.com)
  • Sequence similarity is a powerful tool for discovering biological function. (oreilly.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)
  • Analysis of DNA sequence similarity within organisms causing New World leishmaniasis / by Jesús Alexis Mendoza León. (who.int)
  • 2] Manoj Kumar Gupta, R. Niyogi and M. Misra, "An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition," SAR and QSAR in Environmental Research, vol. 24 (7), pp. 597-609, 2013, Taylor and Francis. (smvdu.ac.in)
  • 3] Manoj Kumar Gupta, R. Niyogi and M. Misra, "A 2D graphical representation of protein sequence and their similarity analysis with probabilistic method," MATCH Commun. (smvdu.ac.in)
  • BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (addgene.org)
  • 2003. " Manifold: Protein Fold Recognition Based On Secondary Structure, Sequence Similarity And Enzyme Classification " . (uni-heidelberg.de)
  • In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. (osti.gov)
  • TotalSeq-D reagents are compatible with Illumina® sequencing platforms. (biolegend.com)
  • Genome sequencing on the Illumina platform was performed as previously described [ 8 ]. (jgenomics.com)
  • Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and explore the possible antiviral properties of these protein ligand complexes. (chemrxiv.org)
  • In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the SARS-CoV-2 whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible binding with ligands that exhibit antiviral properties. (chemrxiv.org)
  • The C-terminus of cytochrome c'' has homology with the corresponding region of an oxygen-binding haem protein (SHP) from phototrophically grown Rhodobacter sphaeroides. (unl.pt)
  • This is because the functionality, processing, localization and stability of RNAs are all dependent on the folding of these molecules into intricate structures through specific base pairing interactions encoded in their primary nucleotide sequences. (upenn.edu)
  • Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
  • Nucleotide sequences were initially checked using the Basic Local Alignment Search Tool hosted by the National Center for Biotechnology Information ( http://blast.ncbi.nlm.nih.gov/Blast.cgim ) for comparison with other known nucleotide sequences. (who.int)
  • Therefore we concluded the possible effect that the mutation could have on the protein. (tu-muenchen.de)
  • Mutation analysis shows base substitution (A-->G) in the consensus splice donor sequence linked to exon 14 resulting in the skipping of exon 14 and the splicing of exon 13-15. (cdc.gov)
  • The effect of nmf19 mutation is expected to be severe since the expressed Pcdh15 protein is predicted to truncate in the 5th cadherin domain. (cdc.gov)
  • Typically, databases of related proteins focus on those from completely-sequenced genomes. (uni.lu)
  • Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. (oreilly.com)
  • METHODS: We performed a meta-analysis of HDL-C within the CETP region using 59,432 individuals imputed with 1000 Genomes data. (eur.nl)
  • To identify if there are distinguishing mutations in the African SARS-CoV-2 genomes compared to genomes from other countries, including disease hotspots, we conducted in silico analyses and comparisons. (bvsalud.org)
  • This study shows for the first time, an in-depth analysis of the SARS-CoV-2 landscape across Africa and will potentially provide insights into specific mutations to relevant proteins in the SARS-CoV-2 genomes in African populations. (bvsalud.org)
  • SAVoR: A Server for Sequencing Annotation and Visualization of RNA Str" by Fan Li, Paul Ryvkin et al. (upenn.edu)
  • Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. (nih.gov)
  • Ahmed MS, Islam MA, Hossain MM, Nasreen M. An In Silico Approach for Characterization of an Acetyltransfarase Protein from Shigella flexneriSerotype 5b (strain 8401). (avensonline.org)
  • A hypothetical protein yjaB of these bacteria, consisting of 147 residues was picked out for in silico analysis. (avensonline.org)
  • Previously we have designed (by in silico structure-based analysis) three very short peptides having sequences inspirited by hACE2 native fragments, which effectively bind to the SARS-CoV-2 S protein and block its interaction with the human receptor. (waw.pl)
  • The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). (nih.gov)
  • In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. (osti.gov)
  • It is one of the most important software packages used in sequence analysis and bioinformatics. (oreilly.com)
  • Bioinformatics approach is an alternative to laboratory-based methods that makes of algorithms and databases to predict protein function. (avensonline.org)
  • By using high performance sequencing and bioinformatics analyses, this work characterizes microRNAs produced by Paracoccidioides brasiliensis. (figshare.com)
  • Molecular genetic analysis of brassinosteroid action. (ncsu.edu)
  • Resolve complex genetic questions from genotype to phenotype by combining single-cell genetic analysis with protein detection using TotalSeq™-D oligo-conjugated reagents. (biolegend.com)
  • Uncover genetic variations in heterogenous samples using Mission Bio's Tapestri platform and add BioLegend's TotalSeq-D antibodies to correlate these mutations with protein expression. (biolegend.com)
  • Cell genetic analyses of the induction reveal that it requires AhR and Arnt. (cdc.gov)
  • For example, one child diagnosed by genome sequencing with early infantile epileptic encephalopathy type 11, a severe, genetic form of epilepsy that is amenable to treatment with a ketogenic diet, was switched to a high-fat diet, which reduced the frequency of seizures. (cdc.gov)
  • The genetic change found in this population deletes several amino acids and replaces them with other amino acids at the end of the titin protein. (medlineplus.gov)
  • Whole genome sequence data of 2 belted and 130 control cattle yielded only one private genetic variant in the critical interval in the two belted animals. (plos.org)
  • 1998. " Implementing Genetic Algorithms With Sterical Constraints For Protein Structure Prediction " . (uni-heidelberg.de)
  • Combining genetic analysis with structural modeling of specific Tudor domains, we propose that these domains serve as `docking platforms' for polar granule assembly. (biologists.com)
  • KIAA1549-BRAF fusion is the most common genetic event in pilocytic astrocytoma (PA), and leads to activation of the mitogen activated protein kinase (MAPK) signaling pathway. (vdocuments.mx)
  • Results from this study could expand the scope of genetic counselling which currently focuses mainly on mutations that truncate and destroy the protein. (who.int)
  • These are usually small peptides, with a size comprised between 11 and 50 amino acids, and which are often released by the cleavage of larger protein precursors (or pro-proteins). (frontiersin.org)
  • Polymorphisms that slightly vary native peptides or inflammatory processes set the stage for abnormal protein folding and amyloid fibril deposition. (medscape.com)
  • Using HOCl-oxidized lysozyme as a model system, it was found that the immonium ions of oxidized tyrosine and tryptophan formed in MS(2) analysis could not be used as diagnostic ions, owing to the occurrence of isobaric fragment ions from unmodified peptides. (aston.ac.uk)
  • This release contains forward-looking information about, among other things, our efforts to advance wellness, prevention, treatments and cures that challenge the most dominant surface proteins expressed by the Broad avalide nombre generico Institute of MIT and Harvard, the browser gives access to results from analyses of whole exome sequencing data has been filed with the transition. (antiwaft.com)
  • Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. (semanticscholar.org)
  • Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. (chemrxiv.org)
  • The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation. (nih.gov)
  • Protein characterization has become an integral part of modern biology, even inspiring a new discipline known as proteomics, or the classification of proteins based on the genome of an organism. (warf.org)
  • CHAPTER 5: Sporulation phosphorelay proteins and their complexes: Crystallographic characterization. (elsevier.com)
  • The Pittsburgh Supercomputing Center is offering a NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS workshop, July 20-25, 1997. (bio.net)
  • Direct sequencing of the pan-flavavirus PCR amplicons showed Usutu virus nucleic acid sequences in each sample. (cdc.gov)
  • In the 1980s, biochemical analysis of the nucleic acid composition of Pneumocystis rRNA and mitochondrial DNA identified the organism as a unicellular fungus rather than a protozoan. (medscape.com)
  • For protein sequencing, we have utilized both targeted and non-targeted protein detection using nanoflow liquid chromatography-high resolution, accurate mass-tandem mass spectrometry. (ishinews.com)
  • Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (nih.gov)
  • Tandem mass spectrometry (MS/MS) is a technique capable of identifying large numbers of proteins in complex biological samples. (warf.org)
  • Background In epigenetic analysis, both the increasing ease of high-throughput sequencing and a greater desire for genome-wide studies possess resulted in an exponential flooding of epigenetic-related data in public domain. (rawveronica.com)
  • BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. (oreilly.com)
  • We used high-throughput DNA sequencing analysis to generate 4258 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5′ (97) and 3′ (4161) ends of human cDNA clones from a HBMSC cDNA library. (elsevier.com)
  • These experiments provide a foundation for identifying virulence associated surface proteins of this important pathogen and have generated immunological reagents that will allow us to characterize these bacteria during disease. (usda.gov)
  • In the present work we characterize the trimeric TPR-containing protein YbgF, which is linked to the Tol system in Gram-negative bacteria. (ox.ac.uk)
  • Our study lays the foundations for understanding the structural basis for TPR domain self-association and how such self-association can be regulated in TPR domain-containing proteins. (ox.ac.uk)
  • Analysis of worldwide sequence mutations in Zika virus proteins E, NS1, NS3 and NS5 from a structural point of view. (bvsalud.org)
  • We present here an analysis of all ZIKV sequences available in Genbank up to April 2016, studying the mutations in the whole polyprotein and their possible structural implications for the proteins E, NS1, NS3 and NS5. (bvsalud.org)
  • Many mechanisms of protein function contribute to amyloidogenesis, including "nonphysiologic proteolysis, defective or absent physiologic proteolysis, mutations involving changes in thermodynamic or kinetic properties, and pathways that are yet to be defined. (medscape.com)
  • We collected the family history and detailed clinical information, then performed whole-exome sequencing, and analyzed the pathogenicity of the candidate mutations. (biomedcentral.com)
  • We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment. (jax.org)
  • Mutations that affect the function of the ATM protein, without destroying the protein, were found to confer the highest risk of breast cancer. (who.int)
  • It was found that a class of substitutions in the DNA sequence of the ATM protein that alter amino acids (known as missense mutations) have a greater association with breast cancer than expected. (who.int)
  • Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia. (cdc.gov)
  • Four isolates (designated strains TC112, TC129, TC147, and TC273) cultured from bovine urine during that study have now been fully sequenced and are compared herein. (jgenomics.com)
  • Polymerase chain reaction (PCR) was conducted using groEL PCR-restriction fragment length polymorphism and sequence analysis. (who.int)
  • Full-length genome sequence of this putative novel Usutu virus strain, designated Usutu-BONN, was successfully attained. (cdc.gov)
  • In conclusion, the authors detected and genetically characterized a putative novel Usutu virus strain (Usutu-BONN) by determining its complete genome sequence and comparing it with Usutu virus strains for which complete polyprotein-encoding sequences are available. (cdc.gov)
  • Here, we report and compare the complete genome sequence of four recent isolates of L . borgpetersenii serovar Hardjo designated strain TC112, TC147, TC129, and TC273. (jgenomics.com)
  • All genome sequence information is available on GenBank ( https://www.ncbi.nlm.nih.gov/genbank/ ), BioProject PRJNA759631. (jgenomics.com)
  • The interaction effects between different proteins are illustrated by four different lines representing binding, secreted/express, phosphorylation, and activation. (biomedcentral.com)
  • Ublast hits may be split across two different proteins. (lbl.gov)
  • Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques. (ncsu.edu)
  • C9ORF135 encodes a membrane protein whose expression is related to pluripotency in human embryonic stem cells. (nih.gov)
  • Little is known about the structure or protein constituents of the Brachyspira pilosicoli outer membrane (OM). (usda.gov)
  • In order to identify surface exposed proteins in this species, membrane vesicles were isolated from B. pilosicoli strain 95-1000 cells by osmotic lysis in distilled water followed by isopycnic centrifugation in sucrose density gradients. (usda.gov)
  • Detergent phase partitioning in Triton X-114 suggests the 24 kDa and 35 kDa proteins are integral membrane proteins. (usda.gov)
  • Among multiple encoded proteins (structural, non-structural, and accessory), four major structural proteins are the spike (S) glycoprotein, small envelope protein (E), membrane protein (M), and nucleocapsid protein (N) ( Ahmed, Quadeer & McKay, 2020 ). (peerj.com)
  • Membrane proteins roughly constitute 30% of open reading frames in a genome and form 70% of current drug targets. (iisc.ac.in)
  • They are classified as integral, peripheral membrane proteins and polypeptide toxins. (iisc.ac.in)
  • This protein-protein recognition process is involved in the early stages of the SARS-CoV-2 life cycle leading to the host cell membrane penetration. (waw.pl)
  • Prediction of residues involved in external protein-protein interactions. (rostlab.org)
  • Protein interactions, docking and function. (wikicfp.com)
  • Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)
  • [ 4 ] It is also important to understand that the same polypeptide sequence can produce many different patterns of interresidue or intraresidue interactions. (medscape.com)
  • Specifically, under BioStrength we setup and operate the Cell Imaging and Biomolecular Interactions (CiBIT) core facility, a high-end unit which focuses in the areas of Bioimaging and Biomolecular interaction analysis. (europa.eu)
  • Tudor domains are found in many organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. (biologists.com)
  • The peptide-based strategy is rapid and cost-effective for developing and optimizing efficient protein-protein interactions disruptors and may be successfully applied to discover antiviral candidates against other future emerging human viral infections. (waw.pl)
  • [ 5 ] In humans, about 23 different unrelated proteins are known to form amyloid fibrils in vivo. (medscape.com)
  • This intense workshop will teach the basics of sequence analysis, including remote supercomputing, database searching and pairwise sequence alignment, multiple sequence alignments, pattern identification, inverse structure prediction, and visualization of macromolecular structures. (bio.net)
  • 1999. " Ab Initio Protein Structure Prediction With Molego " . (uni-heidelberg.de)
  • 2000. " Protein Structure Prediction Using Combinatorial Optimization " . (uni-heidelberg.de)
  • 1998. " Protein Structure Prediction With Combinatorial Optimization " . (uni-heidelberg.de)
  • In Third Community Wide Experiment On The Critical Assessment Of Techniques For Protein Structure Prediction, Casp3 , 77. (uni-heidelberg.de)
  • Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. (princeton.edu)
  • It is a user-friendly, stand-alone computational system designed to support multiple datasets, for carrying out genome-wide correlative and quantitative analysis of ChIP-seq and RNA-seq data. (rawveronica.com)
  • However, we state that structural formulas can be regarded as abstract representations emerging from the analysis of large amounts of data upon chemical reactivity. (benthamscience.com)
  • Protein count data were transformed and visualized in a UMAP projection overlaid with protein. (biolegend.com)
  • Thus, as the number of RNA sequencing (RNA-seq) data sets and the variety of protocols for this technology grow rapidly, it is becoming increasingly pertinent to develop tools that can analyze and visualize this sequence data in the context of RNA secondary structure. (upenn.edu)
  • SAVoR accepts read alignment data from RNA-seq experiments and computes a series of per-base values such as read abundance and sequence variant frequency. (upenn.edu)
  • All raw and analyzed sequencing data can be found at the NCBI Sequence Read Archive ( PRJNA604208 ). (nature.com)
  • Hits to curated proteins without experimental data as to their function are never considered high confidence. (lbl.gov)
  • The data presented in this study suggest the utility of phylogenetic analysis of the amino acid sequence of E-NS1 junction region for molecular epidemiology of dengue viruses. (who.int)
  • Delhi epidemic of 1967 and compared the appears to be no particular region of data with other published sequences of DEN- hypervariability. (who.int)
  • Whole genome sequencing data and RNA-seq data from this study have been submitted to the European Nucleotide Archive under accessions PRJEB14604 and PRJEB14606. (plos.org)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
  • Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
  • The analysis of NHANES laboratory data must be conducted with the key survey design and basic demographic variables. (cdc.gov)
  • For the past three years, Signature Science has been working on the IARPA PROTEOS program to demonstrate that protein sequencing can successfully be used for human forensic identification for samples where DNA was either absent or degraded, specifically touch samples. (ishinews.com)
  • Numerous samples yielded insufficient DNA for comparison but supplied sufficient protein for correct identification against a panel of 52 potential contributors. (ishinews.com)
  • Identification and functional analysis of tomato BRI1 and BAK1 receptor kinase phosphorylation sites. (ncsu.edu)
  • Identification and functional analysis of in vivo phosphorylation sites of the Arabidopsis brassinosteroid-insensitive1 receptor kinase. (ncsu.edu)
  • Phylogenetic analysis showed the single-domain FKBPs to evolve prior to the multi-domain FKBPs, whereas the multi-domain cyclophilins appear to evolve throughout cyclophilin evolution. (biomedcentral.com)
  • The phylogenetic analysis had been reported since 1967(4). (who.int)
  • Phylogenetic analysis demonstrated that Usutu bond constitutes a putative novel African Usutu virus lineage, which was probably, recently, introduced to Central Europe. (cdc.gov)
  • The possibility of an African origin of this virus strain is strengthened by the fact that phylogenetic analysis of complete polyprotein sequence established a separate basal lineage for the Usutu-BONN strain in a sister relationship with the African Usutu virus strains. (cdc.gov)
  • Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible targets for vaccine coverage or potential therapeutic agents. (bvsalud.org)
  • In contrast, protein unfolding adds new residues to the unstructured pool of amino acids, making titin more elastic. (nature.com)
  • An insert of eight amino acids (represented by positions 69-76) was confirmed between residues corresponding to positions 69 and 70 of human protein AA, which is consistent with the previously reported sequence in non-Shar-pei breeds. (umn.edu)
  • Precursor ion scanning for fragment ions of oxidized amino acid residues was investigated as a label-free MS approach to mapping specific oxPTMs in a complex mixture of proteins. (aston.ac.uk)
  • Multiple sequence alignment (MSA) was used to locate the conserved residues. (avensonline.org)
  • Proteins are large biomolecules consisting of one or more long chains of amino acid residues. (iisc.ac.in)
  • Crafting these residues, which are located in loop regions between TPR motifs, onto the monomeric consensus TPR protein CTPR3 induced the formation of oligomers. (ox.ac.uk)
  • Introduction to sequence alignment. (mit.edu)
  • BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. (oreilly.com)
  • Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. (zugaina.org)
  • Proteomics also aided in the analysis of mixed contributor samples, highlighted by one example where a contributor who was not identified in the DNA mixture was identified using protein markers. (ishinews.com)
  • Proteomics is a relatively new discipline that is a large scale study of proteins. (warf.org)
  • Statistical analysis of alignments of large numbers of protein sequences has revealed 'sectors' of collectively coevolving amino acids in several protein families. (princeton.edu)
  • Database searching continued, and introduction to multiple sequence alignments. (mit.edu)
  • In both types of analyses, the outcomes determined two types of clusters: a repressive cluster designated by a solid relationship between Polycomb protein (Suz12 and Ezh2) and their related histone PTMs (H3K27me3), and elements and histone PTMs connected with energetic transcription (H3K27ac, H3K9ac, Pol2, H3K79me2). (rawveronica.com)
  • Generating clusters based only on individual proteins of interest is less time consuming than generating clusters for whole proteomes. (uni.lu)
  • Clusters were identified based on protein expression only. (biolegend.com)
  • Workflow for comparative analysis of sequence evolution and structural dynamics is shown. (pitt.edu)
  • Workflow for GNM analysis of chromatin dynamics. (pitt.edu)
  • To overcome this hurdle, we developed a workflow that allows protein to be recovered following a conventional DNA collection and silica column-based extraction. (ishinews.com)
  • Furthermore, the developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. (osti.gov)
  • Human PBMCs were stained with the TotalSeq-D Heme Oncology Cocktail v1.0 and processed using the Mission Bio Tapestri DNA and Protein workflow. (biolegend.com)
  • An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. (peerj.com)
  • We will focus on sequence analysis, genomics, and protein folding. (mit.edu)
  • Light-chain proteins in the urine cannot be detected using Albustix or other dipstick methods. (medscape.com)
  • Perform the Putnam heat test or the sulfosalicylic acid (SSA) test (with Exton reagent) to help detect urinary light-chain proteins. (medscape.com)
  • Light-chain proteins are best detected and identified using immunoelectrophoresis with monospecific antikappa and antilambda sera. (medscape.com)
  • Light-chain proteins appear in urine in high concentration either when the production of light-chain proteins is markedly increased or when the ability of the proximal tubules to reabsorb all the filtered protein is diminished. (medscape.com)
  • The presence of light-chain proteins in the urine is associated with a number of systemic diseases (see Etiology ). (medscape.com)
  • The kidney is the major site of metabolism of light-chain proteins. (medscape.com)
  • The filtered light-chain proteins, reabsorbed by the proximal tubular cells via the tandem megalin/cubilin receptors, are catabolized by lysosomal enzymes. (medscape.com)
  • Metabolism (catabolism) of these filtered light-chain proteins depends on normal proximal tubular cell function, and damage to these cells can result in increased excretion of light-chain proteins in the urine. (medscape.com)
  • Revealing evolutionary constraints on proteins through sequence analysis. (princeton.edu)
  • Evolutionary constraints on the trajectories are reflected at the molecular level, and can be probed by a number of techniques including biochemistry and comparative analysis of extant successful protein sequences. (evocellnet.com)
  • To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. (osti.gov)
  • Computational protein design is becoming a powerful tool for tailoring enzymes for specific biotechnological applications. (researchgate.net)
  • Durbin, Richard is the author of 'Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids', published 1999 under ISBN 9780521629713 and ISBN 0521629713. (valorebooks.com)
  • Antibody reagents to detect specific proteins were prepared and shown to react with surface proteins. (usda.gov)
  • Each antibody is conjugated to an oligonucleotide that consists of a capture sequence, clone-specific barcode sequence, and a PCR handle. (biolegend.com)
  • Each lot of this antibody is quality control tested by immunofluorescent staining with flow cytometric analysis and the oligomer sequence is confirmed by sequencing. (biolegend.com)
  • Renowned as the #1 antibody event in the industry, this year's agenda boasts 15 dedicated topic streams, 3 unmissable training course add-on options and will bring together more than 700 of the antibody and protein community. (cshlpress.org)
  • Light chains are divided into 2 major classes based on the amino acid sequence in the constant portion of the polypeptide chain and are designated as kappa and lambda. (medscape.com)
  • These are further divided into at least 10 subtypes (4 kappa and 6 lambda) based on the amino acid sequence in the variable region of the polypeptide chain. (medscape.com)
  • CD69 is a 27-33 kD type II transmembrane protein also known as activation inducer molecule (AIM), very early activation antigen (VEA), and MLR3. (biolegend.com)
  • DRAM2 encodes a transmembrane lysosomal protein thought to play a role in the initiation of autophagy. (ox.ac.uk)
  • This event is prevented by small Heat Shock Proteins (sHSPs) acting as molecular chaperones. (iisc.ac.in)
  • Small heat shock proteins (sHSPs) are a ubiquitous family of molecular chaperones that play a vital role in maintaining protein homeostasis in cells. (iisc.ac.in)
  • By measuring the levels of heat shock proteins as well as the activation of mitogen activated protein kinases (MAPKs), we could not detect any differences upon RF exposure. (bvsalud.org)
  • The impact of the resulting protein alterations was assessed in a methylation tolerance-based assay. (bmj.com)
  • A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. (biomedcentral.com)
  • mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. (biomedcentral.com)
  • Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. (biomedcentral.com)
  • Northern blot analysis suggests that wild-type amounts of an apparently normal 2.3-kb transcript accumulate in mutant cells during flagellar regeneration. (rupress.org)
  • Here, we demonstrated that the transcript encoding proteins involved in microRNA biogenesis were differentially expressed in each morphological stage. (figshare.com)
  • Conclusions EpiMINE performs different kinds of genome-wide quantitative and correlative analyses, using ChIP-seq- and RNA-seq-related datasets. (rawveronica.com)
  • Many bioinformatic tools were used to predict the 3D structure and function of this protein. (avensonline.org)
  • Histones, confirmed by sequence analysis, were present in several SDS-PAGE bands (molecular masses of approximately 18.5, 17.5, and 13 kDa) from purified renal medullary amyloid of one Shar-pei dog. (umn.edu)
  • Several Tud domain proteins have been shown to interact with modified histones. (biologists.com)
  • In this strain, 1 putative cleavage site of the viral polyprotein responsible for processing of structural proteins was changed. (cdc.gov)
  • METTL18 is established as the second human histidine-specific protein MTase, and its functional relevance is demonstrated, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. (semanticscholar.org)
  • Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. (princeton.edu)
  • For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. (princeton.edu)
  • The 10 corresponding protein isoforms exhibit either large deletions (49-93 amino acids (aa)), small deletions (12 or 16 aa) or insertions (3-10 aa) within different functional domains. (bmj.com)
  • We performed replication in an independent sample of 47,866 individuals and validation was done by Sanger sequencing. (eur.nl)
  • Sanger sequencing of the insertion within a single family confirmed segregation of this variant. (eur.nl)