The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A 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.
Sequential operating programs and data which instruct the functioning of a digital computer.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The relationships of groups of organisms as reflected by their genetic makeup.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The act of testing the software for compliance with a standard.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
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.
Computer-assisted analysis and processing of problems in a particular area.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
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 systematic study of the complete DNA sequences (GENOME) of organisms.
Computer-based representation of physical systems and phenomena such as chemical processes.
Databases devoted to knowledge about specific genes and gene products.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
Text editing and storage functions using computer software.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
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.
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
Organized activities related to the storage, location, search, and retrieval of information.
In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)
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.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
A 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.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Specifications and instructions applied to the software.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Specific languages used to prepare computer programs.
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.
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 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.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Software designed to store, manipulate, manage, and control data for specific uses.
Proteins found in any species of bacterium.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Displacement of bones out of line in relation to joints. It may be congenital or traumatic in origin.
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)
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
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.
Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.
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 restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
Genotypic differences observed among individuals in a population.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
The construction or arrangement of a task so that it may be done with the greatest possible efficiency.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
Proteins prepared by recombinant DNA technology.
The study of chance processes or the relative frequency characterizing a chance process.
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.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
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).
The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
A family of parasitic organisms in the order EIMERIIDAE. They form tissue-cysts in their intermediate hosts, ultimately leading to pathogenesis in the final hosts that includes various mammals (including humans) and birds. The most important genera include NEOSPORA; SARCOCYSTIS; and TOXOPLASMA.
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.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Method of measuring performance against established standards of best practice.
Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.
A system for verifying and maintaining a desired level of quality in a product or process by careful planning, use of proper equipment, continued inspection, and corrective action as required. (Random House Unabridged Dictionary, 2d ed)
Any method used for determining the location of and relative distances between genes on a chromosome.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
The genetic complement of a BACTERIA as represented in its DNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
The rate dynamics in chemical or physical systems.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The 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)
Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
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.
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 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.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.
Computerized compilations of information units (text, sound, graphics, and/or video) interconnected by logical nonlinear linkages that enable users to follow optimal paths through the material and also the systems used to create and display this information. (From Thesaurus of ERIC Descriptors, 1994)
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
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).
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
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.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The functional hereditary units of BACTERIA.
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.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A synovial hinge connection formed between the bones of the FEMUR; TIBIA; and PATELLA.
Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem.
Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)
The genetic complement of a plant (PLANTS) as represented in its DNA.
The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.
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.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
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.
Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.
Proteins obtained from ESCHERICHIA COLI.
DNA-binding domains present in proteins of the HMG-box superfamily including the archetypal HMGB PROTEINS, a number of sequence specific TRANSCRIPTION FACTORS, and other DNA-BINDING PROTEINS. The domains consist of 70-80 amino acids that form an L-shaped fold from three alpha-helical segments. The domain has the capacity to recognize and/or induce specific DNA structures and effect the accessibility of the DNA to other proteins involved in transcription, recombination, or DNA repair. (Note that not all HIGH MOBILITY GROUP PROTEINS contain this domain.)
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.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
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.
Biochemical identification of mutational changes in a nucleotide sequence.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".
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.
Proteins found in any species of virus.
A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.
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.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
An agency of the NATIONAL INSTITUTES OF HEALTH concerned with overall planning, promoting, and administering programs pertaining to advancement of medical and related sciences. Major activities of this institute include the collection, dissemination, and exchange of information important to the progress of medicine and health, research in medical informatics and support for medical library development.
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.
An essential amino acid that is required for the production of HISTAMINE.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Proteins found in any species of archaeon.
Transport proteins that carry specific substances in the blood or across cell membranes.
The process of generating three-dimensional images by electronic, photographic, or other methods. For example, three-dimensional images can be generated by assembling multiple tomographic images with the aid of a computer, while photographic 3-D images (HOLOGRAPHY) can be made by exposing film to the interference pattern created when two laser light sources shine on an object.
The characteristic three-dimensional shape of a molecule.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
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.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Surgical procedures conducted with the aid of computers. This is most frequently used in orthopedic and laparoscopic surgery for implant placement and instrument guidance. Image-guided surgery interactively combines prior CT scans or MRI images with real-time video.
Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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 accumulation of an electric charge on a object
A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
Methods for determining interaction between PROTEINS.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
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.
The second longest bone of the skeleton. It is located on the medial side of the lower leg, articulating with the FIBULA laterally, the TALUS distally, and the FEMUR proximally.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
A genus of anaerobic coccoid METHANOCOCCACEAE whose organisms are motile by means of polar tufts of flagella. These methanogens are found in salt marshes, marine and estuarine sediments, and the intestinal tract of animals.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
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.
Elements of limited time intervals, contributing to particular results or situations.

Intracellular signalling: PDK1--a kinase at the hub of things. (1/38700)

Phosphoinositide-dependent kinase 1 (PDK1) is at the hub of many signalling pathways, activating PKB and PKC isoenzymes, as well as p70 S6 kinase and perhaps PKA. PDK1 action is determined by colocalization with substrate and by target site availability, features that may enable it to operate in both resting and stimulated cells.  (+info)

Molecular phylogeny of the ETS gene family. (2/38700)

We have constructed a molecular phylogeny of the ETS gene family. By distance and parsimony analysis of the ETS conserved domains we show that the family containing so far 29 different genes in vertebrates can be divided into 13 groups of genes namely ETS, ER71, GABP, PEA3, ERG, ERF, ELK, DETS4, ELF, ESE, TEL, YAN, SPI. Since the three dimensional structure of the ETS domain has revealed a similarity with the winged-helix-turn-helix proteins, we used two of them (CAP and HSF) to root the tree. This allowed us to show that the family can be divided into five subfamilies: ETS, DETS4, ELF, TEL and SPI. The ETS subfamily comprises the ETS, ER71, GABP, PEA3, ERG, ERF and the ELK groups which appear more related to each other than to any other ETS family members. The fact that some members of these subfamilies were identified in early metazoans such as diploblasts and sponges suggests that the diversification of ETS family genes predates the diversification of metazoans. By the combined analysis of both the ETS and the PNT domains, which are conserved in some members of the family, we showed that the GABP group, and not the ERG group, is the one most closely related to the ETS group. We also observed that the speed of accumulation of mutations in the various genes of the family is highly variable. Noticeably, paralogous members of the ELK group exhibit strikingly different evolutionary speed suggesting that the evolutionary pressure they support is very different.  (+info)

Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. (3/38700)

The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes.  (+info)

A single membrane-embedded negative charge is critical for recognizing positively charged drugs by the Escherichia coli multidrug resistance protein MdfA. (4/38700)

The nature of the broad substrate specificity phenomenon, as manifested by multidrug resistance proteins, is not yet understood. In the Escherichia coli multidrug transporter, MdfA, the hydrophobicity profile and PhoA fusion analysis have so far identified only one membrane-embedded charged amino acid residue (E26). In order to determine whether this negatively charged residue may play a role in multidrug recognition, we evaluated the expression and function of MdfA constructs mutated at this position. Replacing E26 with the positively charged residue lysine abolished the multidrug resistance activity against positively charged drugs, but retained chloramphenicol efflux and resistance. In contrast, when the negative charge was preserved in a mutant with aspartate instead of E26, chloramphenicol recognition and transport were drastically inhibited; however, the mutant exhibited almost wild-type multidrug resistance activity against lipophilic cations. These results suggest that although the negative charge at position 26 is not essential for active transport, it dictates the multidrug resistance character of MdfA. We show that such a negative charge is also found in other drug resistance transporters, and its possible significance regarding multidrug resistance is discussed.  (+info)

Anopheles gambiae Ag-STAT, a new insect member of the STAT family, is activated in response to bacterial infection. (5/38700)

A new insect member of the STAT family of transcription factors (Ag-STAT) has been cloned from the human malaria vector Anopheles gambiae. The domain involved in DNA interaction and the SH2 domain are well conserved. Ag-STAT is most similar to Drosophila D-STAT and to vertebrate STATs 5 and 6, constituting a proposed ancient class A of the STAT family. The mRNA is expressed at all developmental stages, and the protein is present in hemocytes, pericardial cells, midgut, skeletal muscle and fat body cells. There is no evidence of transcriptional activation following bacterial challenge. However, bacterial challenge results in nuclear translocation of Ag-STAT protein in fat body cells and induction of DNA-binding activity that recognizes a STAT target site. In vitro treatment with pervanadate (vanadate and H2O2) translocates Ag-STAT to the nucleus in midgut epithelial cells. This is the first evidence of direct participation of the STAT pathway in immune responses in insects.  (+info)

Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers. (6/38700)

Gene expression in higher eukaryotes appears to be regulated by specific combinations of transcription factors binding to regulatory sequences. The Ets factor PU.1 and the IRF protein Pip (IRF-4) represent a pair of interacting transcription factors implicated in regulating B cell-specific gene expression. Pip is recruited to its binding site on DNA by phosphorylated PU.1. PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative alpha-helix in Pip. Thus, a coordinated set of protein-protein and protein-DNA contacts are essential for PU.1-Pip ternary complex assembly. To analyze the function of these factors in vivo, we engineered chimeric repressors containing the ets and IRF DNA-binding domains connected by a flexible POU domain linker. When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin lambda gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression. Comparative analysis of the wild-type dimer with a series of mutant dimers distinguished a gene regulated by PU.1 and Pip from one regulated by PU.1 alone. This strategy should prove generally useful in analyzing the function of interacting transcription factors in vivo, and for identifying novel genes regulated by such complexes.  (+info)

Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. (7/38700)

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

The mouse Aire gene: comparative genomic sequencing, gene organization, and expression. (8/38700)

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

Bone malalignment can occur in any bone of the body but is most common in the long bones of the arms and legs. There are several types of bone malalignment, including:

* Angular deformity: A deviation from the normal alignment of two bones meeting at a joint.
* Bowing or bending of a bone: A deviation from the normal straight line of a bone.
* Rotational deformity: A twisting or rotating of a bone around its long axis.
* Growth plate deformity: Abnormal growth or development of the growth plates in children and adolescents, leading to misalignment of the bones.

Bone malalignment can cause symptoms such as pain, stiffness, limited mobility, and difficulty performing daily activities. Treatment options for bone malalignment depend on the type and severity of the condition and may include:

* Bracing or casting to help align the bones
* Physical therapy to improve range of motion and strength
* Medications to manage pain and inflammation
* Surgery to correct the deformity and realign the bones.

Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple ... Sequence homology Sequence mining BLAST String searching algorithm Alignment-free sequence analysis UGENE Needleman-Wunsch ... alignments of two query sequences. Pairwise alignments can only be used between two sequences at a time, but they are efficient ... alignment is desired for the long sequence. Fast expansion of genetic data challenges speed of current DNA sequence alignment ...
Alignment-free sequence analysis Cladistics Generalized tree alignment Multiple sequence alignment viewers PANDIT, a biological ... Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological ... Multiple sequence alignment viewers enable alignments to be visually reviewed, often by inspecting the quality of alignment for ... Muscle - MUltiple Sequence Comparison by Log-Expectation T-coffee - multiple sequence alignment. MAFFT - Multiple Alignment ...
... but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment ... alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based ... pairwise or multiple sequence alignment. Alignment-based approaches generally give excellent results when the sequences under ... Alignment-free approaches have been used in sequence similarity searches, clustering and classification of sequences, and more ...
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... Alignment type: local or global *Sequence type: protein or nucleotide *Sequence type: protein or nucleotide Please see List of ... and multiple sequence alignment. See structural alignment software for structural alignment of proteins. * ...
Sequence alignment software DNASTAR Clustal ProbCons AMAP T-COFFEE MAFFT Edgar RC (2004). "MUSCLE: multiple sequence alignment ... A progressive alignment is performed to obtain a multiple sequence alignment like in Stage 1, but it is optimized by only ... MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and ... This continues until there is a multiple sequence alignment of all input sequences at the root of the tree. This stage focuses ...
Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to ... Alignments-The read name, read sequence, read quality, alignment information, and custom tags are all included in this file. ... and alignment method are all included in this section. The alignments section contains alignments that are linked to specific ... Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary ...
"Sequence Alignment". ALIGN. Archived from the original on 11 August 2003. Retrieved 8 May 2013. (All articles with dead ... In humans, these SH3 domains have a common amino acid sequence Asp-Glu-Leu. This sequence motif is also conserved in other ... Sequence identity was calculated using available sequence data and ALIGN software. GRCh38: Ensembl release 89: ENSG00000214193 ...
Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all ... Multiple sequence alignment List of sequence alignment software Structural Classification of Proteins SuperPose Protein ... The structural alignment also implies a corresponding one-dimensional sequence alignment from which a sequence identity, or the ... A recent method for pairwise structural alignment of RNA sequences with low sequence identity has been published and ...
"Clustal Omega". Multiple Sequence Alignment. EMBL-EBI. Retrieved February 17, 2020. "Compute pI/Mw Tool". ExPASy. ... In research, the sequence has been identified as containing a possible pathogenic recessive variant (K53N) for various ... Using the Genomatix tool Gene2Promoter, C16orf90 was found to have 4 possible promoter sequences. The promoter set 3, GXP_ ... The orthologs are sorted by increasing date of divergence and sequence similarity. C16orf90 is limited to mammals but is found ...
"Multiple Sequence Alignment". Multiple Sequence Alignment. ClustalW. "TimeTree of Life". TimeTree. "WebLogo Database". WebLogo ... The sequence always begins with a polar glycine and a hydrophobic valine. There is also a conserved basic arginine within the ... Myristoylation sites are found in the protein sequence 17 times, and a zinc finger domain motif occurs once. The presence of ... Several transcription factors are predicted to bind to the promoter sequence. Some examples include: X-box binding factors ...
"Multiple Sequence Alignment". Clustal Omega. "Basic Local Alignment Search Tool". NCBI. "NCBI Blast". "Clustal ... When multiple sequence alignments were made, the zinc finger binding domains were the areas with the most conservation. ZNF800 ... a BLAT search of the fungus sequence in the human domain gave no results, which lead to the conclusion that these sequences are ... The protein is made in small amounts, potentially due to the unfavorability of its Kozak sequence as compared to that of more ...
"Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". Retrieved 2021-12-09. "Standard Protein BLAST". BLAST. ... "Multiple Sequence Alignment". Clustal Omega. EMBL. "TimeTree". TimeTree. TimeTree. Vogel GF, Klee KM, Janecke AR, Müller T, ... bacteria and protists with available sequences were trp236, arg255, trp259, ile297, asp300, arg303, thr304, leu321, leu325, ...
Point mutation Sequence alignment Margaret Dayhoff Molecular clock BLOSUM BLAST Campbell NA, Reece JB, Meyers N, Urry LA, Cain ... In bioinformatics, PAM matrices are sometimes used as substitution matrices to score sequence alignments for proteins. Each ... Pevsner J (2009). "Pairwise Sequence Alignment". Bioinformatics and Functional Genomics (2nd ed.). Wiley-Blackwell. pp. 58-68. ... are also used as a scoring matrix when comparing DNA sequences or protein sequences to judge the quality of the alignment. This ...
"Multiple Sequence Alignment". ClustalW. Kyoto University Bioinformatics Center. Retrieved 28 March 2018. "BoxShade Server". ...
"Sib Dotlet Sequence Alignment". Retrieved 13 May 2013. Pandey NB, Marzluff WF (Dec 1987). "The stem-loop structure at the 3' ... The following table illustrates the sequence similarity between human c10orf76 protein and various orthologs. Similar sequences ... There are ten conserved potential phosphorylation sites within the protein sequence. Also, there are nine residues that are ... Lupas A, Van Dyke M, Stock J (May 1991). "Predicting coiled coils from protein sequences". Science. 252 (5009): 1162-4. Bibcode ...
An Appraisal of Benchmarks for Multiple Sequence Alignment". Multiple Sequence Alignment Methods. Methods in Molecular Biology ... These tests assess the likelihood of the gene sequence alignment when the reference topology is given as the null hypothesis. ... Given simulated sequences which have HGT, analysis of those sequences using the methods of interest and comparison of their ... The donor sequences are inserted into the host unchanged or can be further evolved by simulation, e.g., using the tools ...
"Multiple Sequence Alignment - CLUSTALW". Retrieved 2018-05-06. "TimeTree :: The Timescale of Life". www.timetree ... The coding sequence for the C15orf39 mRNA is 4443 base pairs long. The C15orf39 gene produces seven mRNA transcripts, with the ... C15orf39's sequence has diverged at a quicker rate than the quickly evolving fibrinogen protein in humans. . . . . . . . ... The phylogenetic tree below, shows the evolutionary relationship of the C15orf39 protein sequence in its orthologs. The graph ...
"Multiple Sequence Alignment - CLUSTALW". Retrieved 2019-08-08. "TimeTree :: The Timescale of Life". ... "BLAST: Basic Local Alignment Search Tool". Retrieved 2019-08-01. Human C1orf21 genome location and ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-45. doi:10.1038/ ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-321. Bibcode:2006Natur.441.. ...
"Multiple Sequence Alignment - CLUSTALW". Retrieved 2018-05-06. "BLAST: Basic Local Alignment Search Tool". blast ... Multiple sequence alignments using ClustalW provided evidence that the DUF in C19orf44 is highly conserved in its orthologs. ... "Multiple Sequence Alignment - CLUSTALW". Retrieved 2018-02-25. Vinayagam A, Stelzl U, Foulle R, Plassmann S, ... The amino acid sequence for C19orf44 was found to be serine rich using tools on EMBL-EBI. Additionally, there is a domain of ...
"Multiple Sequence Alignment - CLUSTALW". Kyoto University Bioinformatics Center. Retrieved 2018-05-06. "Ensembl ... Multiple Sequence Alignment < EMBL-EBI". Retrieved 2018-05-06. "Kann Laboratory- Domain Mapping of Disease ... "FAM71E1 family with sequence similarity 71 member E1 [ Homo sapiens (human) ]". NCBI Gene. "SPIB Gene". ... FAM71E1, also known as Family With Sequence Similarity 71 Member E1, is a protein that in humans is encoded by the FAM71E1 gene ...
"Multiple Sequence Alignment - CLUSTALW". Retrieved 2019-07-03. "TimeTree :: The Timescale of Life". ... "BLAST: Basic Local Alignment Search Tool". Retrieved 2019-08-01. Attribution: Contains public domain ... This structure was predicted by analyzing the amino acid sequence using I-TASSER. The final result can be seen below. Predicted ...
Birney, Ewan (2000). Sequence alignment in bioinformatics. (PhD thesis). University of Cambridge. OCLC 894597337. ... c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. ... More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, ... These include gene finding (e.g. GeneWise) with Ewan Birney and Hidden Markov models for protein and nucleic acid alignment and ...
"Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". Retrieved 2018-05-11. "Multiple Sequence Alignment - ... "SAPS < Sequence Statistics < EMBL-EBI". Retrieved 2018-05-06. "PTM prediction tools". Retrieved 2018-05- ... "FAM219A family with sequence similarity 219 member A [Homo sapiens (human)] - Gene - NCBI". Retrieved 2018-05 ... "BLAST: Basic Local Alignment Search Tool". Retrieved 2018-05-06. "RecName: Full=Protein FAM219B - ...
This was carried out by constructing a multiple sequence alignment of the proteins with their secondary structures (as shown ... Nuclear localization sequence with a Score of 4 in the amino acids 265-279. The amino acid sequence for this region is: ... LRRC57 is exceedingly well conserved, as shown in the sequence annotation to the right. The sequence annotation was created ... "Multiple sequence alignment: Strap". "Redirecting to Phyre2". "Clustal Home Page". Retrieved 4 May 2009. "Home". workbench.sdsc ...
... is a multiple sequence alignment program based on sequence annealing. This approach consists of building up the multiple ... S. Schwartz, A.; Pachter, L. (19 January 2007). "Multiple alignment by sequence annealing". Bioinformatics. 23 (2): e24-e29. ... This program accepts sequences in FASTA format. The output format includes: FASTA format, Clustal. ... alignment one match at a time, thereby circumventing many of the problems of progressive alignment. The AMAP parameters can be ...
See multiple sequence alignment below. Annotated diagram of the TMEM229b gene (with its 3 exons), mature mRNA and protein ... Expressed sequence tag mapping of TMEM229B gene expression indicates that it is ubiquitously expressed throughout the body. ... "NCBI Nuceleotide BLAST". Basic Local Alignment Search. "EST profile: TMEM229B". UniGene. National Library of Medicine. ...
FSA is a multiple sequence alignment program for aligning many proteins or RNAs or long genomic DNA sequences. Along with ... As such, FSA considers alignments to be equivalent if for every position along the sequences in both alignments, the same ... This process can cause issues in alignment because the resulting multiple sequence alignment can and will heavily depend on the ... Most existing programs that run multiple sequence alignment algorithms are based on progressive alignment where the process ...
All Atoms Alignment; SSE -- Secondary Structure Elements Alignment; Seq -- Sequence-based alignment Pair -- Pairwise Alignment ... Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments". BMC Bioinformatics. 14 (24): 24. ... Brown, P.; Pullan W.; Yang Y.; Zhou Y. (Oct 2015). "Fast and accurate non-sequential protein structure alignment using a new ... This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise ...
Bishop, Martin J.; Thompson, Elizabeth A. (20 July 1986). "Maximum likelihood alignment of DNA sequences". Journal of Molecular ... 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 ... For example, the probability of the sequence NN and the state being S 1 {\displaystyle S_{1}} then S 2 {\displaystyle S_{2}} is ...
Sequence databases: import, maintain, view, and export sequences. Multiple sequence alignment: align sequences of DNA, RNA, or ... Sequence alignment software Wright ES (2015). "DECIPHER: harnessing local sequence context to improve protein multiple sequence ... Genome alignment: find and align the syntenic regions of multiple genomes. Oligonucleotide design: primer design for polymerase ... Analyze sequences: find chimeras, detect repeats, predict secondary structure, classify into a taxonomy of organisms or ...
The sequence showing the dress-code regimentation of the commuters on the platform should be compared to the reverie in which ... Tramlink services reusing the railway alignment at Bingham Road commenced on 10 May 2000; the formation is no longer elevated ...
Enclitic personal pronouns may (or may not) combine when they occur in sequence, in the order of subject (in the ergative case ... Ilokano has a morphosyntactic alignment that shares characteristics of both Nominative-accusative and Ergative-absolutive known ... "Tell them." Enclitic personal-pronoun sequences occur with goal-oriented (transitive) verbs: verbs that take both a subject and ... one in a sequence) < naudi, "last" < udi "rear". Moderate The moderate form of an adjective denotes that what is being ...
The chronological sequence of each amino acid sub-unit is the basis for directionality notation in polypeptides; a given ... alignments). An example is the two complementary strands of a DNA double helix, which run in opposite directions alongside each ... The nucleic acid sequences are complementary and parallel, but they go in opposite directions, hence the antiparallel ... Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2017-04-01). "Quadruplex DNA: sequence, topology and structure". Nucleic ...
... this strengthening sequence while taking the opportunity provided by the Expand and Empower practice to observe your alignment ... 111: "Head to Knee" - Head to Knee Sequence is the perfect yoga practice for distance runners. This sequence helps to relieve ... 203: "Triangle" - Triangle sequence is not easy to do perfectly, but it will give great benefit to those who give it an honest ... 201: "Sunbird" - Sunbird sequence wakes up the spine, and energizes the limbs. With cat roll, sunbird and dog poses, this ...
Articles with short description, Short description is different from Wikidata, A-type main-sequence stars, M-type main-sequence ... With a new image in 2014, the configuration and alignment of the dust ring and HR4796A has been nicknamed "Eye of Sauron". In ... indicates that both stars belong to the main sequence and are generating energy through the thermonuclear fusion of hydrogen at ...
4) The backward branch to the retry loop must be to the original sequence.: 48-49 The specification gives an example of how to ... Big-endian and bi-endian variants were defined for support of legacy code bases that assume big-endian alignment.: 9-10 An ... RISC-V guarantees forward progress (no livelock) if the code follows rules on the timing and sequence of instructions: 1) It ... The ISA document recommends that implementors of CPUs and compilers fuse a standardized sequence of high and low multiply and ...
... and the re-alignment of its genera across the entire order Apiales". Molecular Phylogenetics and Evolution. 53 (1): 134-151. ... The present understanding of the Apiales is fairly recent and is based upon comparison of DNA sequences by phylogenetic methods ...
"Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". Retrieved 2019-04-29. "ExPASy: SIB Bioinformatics ... It is also known by the aliases Family with Sequence Similarity 178, Member B, and HSPC234. In total there are 24 exons in the ... "SAPS < Sequence Statistics < EMBL-EBI". Retrieved 2019-04-21. Gene: FAM178B (ENSG00000168754) - Splice variants ... A table of relevant transcription factor binding sites that correspond to the sequence and colors highlighted in the promoter ...
The alignment of this planet's orbit may make it directly detectable via the transit method. Another long-period planet or ... indicating this is an evolved star that has exhausted the supply of hydrogen at its core and left the main sequence of stars ...
... challenged conclusions of Walter by writing that Ulam had only modest influence on early development of sequence alignment ... Ulam's work on non-Euclidean distance metrics in the context of molecular biology made a significant contribution to sequence ... Goad, Walter B (1987). "Sequence Analysis: Contributions of Ulam to Molecular Genetics" (PDF). Los Alamos Science. Los Alamos ...
The signing scheme used in 1980 provided explicit units on advance guide signs, but not on interchange sequence signs or post- ... The route follows the former alignment of US 89, SR 93, and SR 789, back when all three highways traversed through southern ... The route follows the former alignment of US 89, SR 93, and SR 789, back when all three highways traversed through southern ... Explicit units were given not just on advance guide signs, but also on interchange sequence signs, post-interchange ...
"Superior Universal Alignment" killings in 1990s Brazil. The Satanic groups Order of Nine Angles and the Temple of the Black ... study of the images seen in Moche art has enabled researchers to reconstruct the culture's most important ceremonial sequence, ...
2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... "The transforming acidic coiled coil 3 protein is essential for spindle-dependent chromosome alignment and mitotic survival". J ...
... is state-of-the-art in gene sequence alignment. The list of applicable classifiers includes the following: Metric approaches ( ... Cluster analysis, vector space model, Minkowski distances, dynamic alignment) Nearest Neighbor methods (K-nearest neighbors ...
The Madhyandina recension and Kanva recension vary in relative sequencing of the hymns, but both assert the introspective ... balanced alignment of the individual and the social interests, the personal and the organizational goals, the material and the ...
2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... ZWINT is a component of the kinetochore-associated multiprotein complex which is required for correct chromosome alignment ... 2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. Bibcode:2001Natur.414.. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
The letter ⠯ and, for example, is used to write words with the sequence a-n-d in them, such as ⠓⠯ hand. Most braille embossers ... they had the disadvantage that the resulting small number of dots in a text interfered with following the alignment of the ... Unlike print, which consists of mostly arbitrary symbols, the braille alphabet follows a logical sequence. The first ten ... The first four decades are similar in respect that in those decades the decade dots are applied to the numeric sequence as a ...
... mouse and chicken sequences with BLASTZ followed by multiple alignment of the pairwise alignments done with MULTIZ. The highly ... Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, ... Of the 510 identified hCONDELs, only one of these deletions has been shown to remove a 92 bp sequence that is part of a protein ... The loss of this SVZ enhancer region in an hCONDEL may provide further insights into the role of DNA sequence changes that may ...
... a display convention for illustrating the alignment of two DNA or protein sequences. Dot Matrix, a character from the animated ...
The Puala sequence was formed 10,240 ± 40 years BP. The Trancura sequence was formed 8,680 ± 40 years BP and has a similar ... Other volcanoes in the Southern Volcanic Zone have similar alignments, such as Nevados de Chillán and Puyehue-Cordón Caulle. In ... The Carén sequence was formed 3,800 ± 30 years BP. The Correntoso sequence was formed 2,930 ± 30 years BP. The Trancas Negras ... The Puesco sequence was formed 1,650 ± 70 years BP, during the largest known eruption of Quetrupillán. This eruption created a ...
... and noted parallel alignments at various points, generally about four miles north or south of the main line. The alignment of ... "Regional Tertiary sequence stratigraphy and regional structure on the eastern flank of the Central Cascade Range, Washington", ... These are much too correlated to be dismissed as random alignments. But for all of its prominence, there is as yet no ... aligned with the Ship Canal, but offset slightly to the north), the alignment of Ravenna Creek (draining Green Lake southeast ...
The term "precession" typically refers only to this largest part of the motion; other changes in the alignment of Earth's axis- ... Dreyer 1958, p. 204) Instead of proceeding through the entire sequence of the zodiac, the equinoxes "trepidated" back and forth ... a precision which could only have been achieved by their alignment with the stars. " (p. 31) The Egyptians also, says Rice, ...
2012). "Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and ... astrological alignments are significant, animal testing is not appropriate to indicate human effects, anecdotal evidence is an ...
This is done by assigning each satellite a unique binary sequence known as a Gold code. The signals are decoded after ... This was very helpful during development because even with only four satellites, correct alignment means all four are visible ... sequence of ones and zeros) that is known to the receiver. By time-aligning a receiver-generated version and the receiver- ... sequence that is different for each satellite. The receiver must be aware of the PRN codes for each satellite to reconstruct ...
2160 video sequences. The video sequences were encoded using the HM-10.0 HEVC encoder and the JM-18.4 H.264/MPEG-4 AVC encoder ... CABAC bypass alignment, a decoding optimization specific to High Throughput 4:4:4 16 Intra profile. HEVC version 2 adds several ... 2160 10-bit video sequences. The 10-bit video sequences were converted to 8 bits for the Main profile and remained at 10 bits ... For all test sequences, when compared with a 64×64 CTU size, it was shown that the HEVC bit rate increased by 2.2% when forced ...
Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860-921. Bibcode:2001Natur.409.. ... Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. (2009). "Infernal 1.0: Inference of RNA alignments". Bioinformatics. 25 (10): 1335- ... Finn, R. D.; Clements, J.; Eddy, S. R. (2011). "HMMER web server: Interactive sequence similarity searching". Nucleic Acids ... His research interests are in bioinformatics, computational biology and biological sequence analysis. As of 2016[update] ...
... as a sequence of related jobs, usually pursued within a single industry or sector: one can speak for example of "a career in ... For better alignment with personal and organizational values (17%). Personal strengths and capabilities are not a good fit with ...
The first week of operations was disrupted by a sequence of IT failures based around software bugs in the Flight Information ... heading directly east on the IGS would become a crosswind and begin to push the aircraft over and off the runway alignment ...
The Sticklepath Fault runs on a north-west to south-east alignment in the northeast of the national park through both the ... The Cornubian batholith was intruded into the midst of the folded and faulted sedimentary sequence during the early part of the ... The Tavy Basin comprises an upper Devonian and Carboniferous sequence of mudstones and sandstones, together with chert. The ... The Culm Basin comprises a Carboniferous sequence also of mudstones, siltstones and sandstones together with chert and tuffs. ...
Accelerating Protein Sequence Alignment with Different Parallel Hardware Platforms. Title Accelerating Protein Sequence ... A sequential implementation of Smith-Waterman requires quadratic running time with respect to the length of the sequences. As ... Detecting similarities between (RNA, DNA, and protein) sequences is an important part of bioinformatics. Among the algorithms ... We also demonstrate that proper partitioning of the sequences can increase parallelism, which leads to better performance. ...
... [ algorithms, bsd3, library ] [ Propose Tags ] FFI wrappers for global and local string alignment ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... Sequence Viewers. Protein Sequence Alignment View. The Protein Sequence Alignment View provides graphical summaries of the ... Sequence Identity. Block color indicates the full alignment sequence identity using a gradient color from Blue to Dark Grey. ... The third Alignment Reference option is Pairwise. When Pairwise is selected the Protein Sequence Alignment View will focus on ...
... represented by multiple sequence alignments and hidden Markov models (HMMs) ... For UniProt-based alignments, we also add some additional mark-up to the alignments where appropriate. Active site information ... This alignment is coloured according to the ClustalX colouring scheme: Glycine (G). Proline (P). Small or hydrophobic (C,A,V,L, ... These lines are shown below the sequence to which they apply and are marked (SS). . The meaning of each of the symbols is as ...
... performs pairwise alignment and progressively aligns it to a local multiple sequence alignment (MSA) based on the alignment ... The proposed algorithms select appropriate alignment and parameter values based on sequence length, identity and alignment ... Amouda V, Buvaneswari S, Kuppuswami S, Self organizing algorithm for multiple sequence alignment, Onl J Bioinform., 12(1): 74- ... A global multiple sequence alignment algorithm (SOGA) includes 2 new operators which perform a self organizing crossover and ...
... structural or evolutionary relationships between two biological sequences (protein or nucleic acid). ... Learn Bioinformatics Online Pairwise Sequence Alignment is used to identify regions of similarity that may show functional, ...
Multiple Sequence Alignment, Representation Closeness, Representativeness, Sequence Invariance. Abstract. Multiple Sequence ... Survey of the use of genetic algorithm for multiple sequence alignment Authors. * Mohamed Tahar Ben Othman Computer Science ... 12] Miranda, L.A. ; Caetano, M.A.F. ; Melo, A.C.M.A. ; Correa, J.M. ; Bordim, J.L., "Multiple Biological Sequence Alignment ... "Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment", IEEE Transactions on Evolutionary ...
command of alignment for general sequences. Learn more about sequence, alignment ... these just for biological sequences. if not are there anyone wrote a code of sequence alignment for non biological sequences in ... What sequence? If you mean any two numerical sequences which are correlated. Their alignment can be done by using cross ... hi, is there a command of sequence alignment for any sequence generally ? I did not mean swalign or nwalign, ...
To address this discovery-to-function gap, we developed a sequence driven:activity-based hybrid approach for screening venom ... The multiple sequence alignment was performed using ClustalW software89.. Fly stocks. All Drosophila melanogaster flies used in ... improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap ... Multiple sequence alignment. The ConoPrec tool, which is available on the ConoServer website was used to identify similar ...
Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using ...
Why are sequence alignments useful?. *What are the main differences in the algorithms of Global and Local alignment? *Why does ... Pairwise sequence alignment. *Mount, D.W. 2001. Bioinformatics: sequence and genome analysis. Cold Spring Horbor Laboratory ... Find the best alignment between the sequences "WHAT" and "WHY", using the Needleman-Wunsch algorithm, with +1 for a match, -1 ... Pairwise sequence alignments. From Protein Prediction 1 Summer Semester 2016 For Informaticians ...
MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of ... by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical ... representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information ... Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. ...
This vector indicates the base-by-base alignment coverage of a range or set of ranges in the reference sequence in BioObj. , a ... object, and then return the alignment coverage of each of the first 12 base positions of the reference sequence:. % Construct a ... Return base-by-base alignment coverage of reference sequence in BioMap. object ... and both integers are smaller than the length of the reference sequence. StartPos. and EndPos. can also be two column vectors ...
LiBis: an ultrasensitive alignment augmentation for low-input bisulfite sequencing.. Yin, Yue; Li, Jia; Li, Jin; Lee, Minjung; ... We developed LiBis (Low-input Bisulfite Sequencing), a novel method for low-input WGBS data alignment. By dynamically clipping ... The resulting low sequencing depth and low coverage of CpG sites genome-wide is a bottleneck for the clinical application of ... Whole-genome bisulfite sequencing (WGBS) is the gold standard for measuring DNA methylation; however, WGBS using small amounts ...
Sequence Alignment. include consensus sequence. ?. Format:. Hypertext. Plain Text. mFasta. Compact Hypertext. Compact Text. Row ...
Use Basic Local Alignment Search Tool (BLAST) via the NCBI website to determine similarity between a given sequence and ... To select a portion of sequence, click one location on the sequence and then a second location to display the sequence between ... BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. Click on the buttons below ... The sequence clipboard box will appear with the top strand sequence of the selected region. To deselect, click back on the ...
Is it possible to get hg18 alignments to panTro2 on the server? ... galaxy-user] Fetch sequence and alignments: extract blastz ...
Sequence Alignment * Sequence Analysis, DNA * Simian Acquired Immunodeficiency Syndrome / virology* * Simian Immunodeficiency ... In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by ... Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral ...
... a high abundance of fungal sequences in samples collected from SFP and FTC. Analysis of the ribosomal internal transcribed ... the assessment of the biological function found a higher proportion of protein-coding sequences related to respiration and ... Molecular characterization was performed using massively parallel sequencing to obtain a taxonomic and functional gene ... Sequence alignment Is the Subject Area "Sequence alignment" applicable to this article? Yes. No. ...
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. ... Analysing high-throughput sequencing data in Python with HTSeq 2.0.. Bioinformatics. 2022; 38: 2943-2945. View in Article * ... DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.. Genome Res. 2013; 23: 341-351. View in Article * ... deepTools2: a next generation web server for deep-sequencing data analysis.. Nucleic Acids Res. 2016; 44: W160-W165. View in ...
Sequence alignment corresponded to.... Samples with the 350-bp amplicon were further investigated by PCR assay with Borrelia ... For comparison, intragroup sequence differences were ≤1.9%. On this basis, as well as the finding of partial IGS sequences ( ... with an available 16S rDNA sequence in the GenBank database. Its partial 16S rDNA sequence differed by 3.3% to 4.2% from 9 LB ... The 788-bp sequence was aligned with sequences of other Borrelia species representing the LB and relapsing fever clades, and ...
Structure-base sequence alignment of SWIRM domain subtypes. The sequence alignment was produced using Cluatal X. Resulting ... Amino acid sequences of SWIRM domain in fasta formats were used for multiple sequence alignment by ClustalX [25] and then ... we performed multiple sequence alignments of the 11 amino acids sequences of SWIRMs from Oryza sativa. These 11 SWIRM domains ... a) Alignment of the SWIRM domain sequences in Oryza sativa. The coloring represents the conservation profile of amino acid ...
Tools for sequence and alignment manipulation Python 8 2 * splitaake Public demultiplex massively parallel sequencing data ...
Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to ... Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. ...
A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional ... Figure 1. Three-dimensional structure of NifF and sequence alignment. (A) Secondary elements and transparent surface of Rc-NifF ... The FMN is represented as balls and sticks in beige; (B) Sequence alignment of most remarkable segments of NifF from R. ... Figure 1. Three-dimensional structure of NifF and sequence alignment. (A) Secondary elements and transparent surface of Rc-NifF ...
Top Sequence Alignment Hits. Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search ... against the protein sequence for RRP4. Description. E-value. Query. Range. Subject. Range. ...
Sequence alignment and analysis * Nucleotide and amino acid sequence alignment. * Whole genome sequence alignment ... High Throughput Sequence analysis (metagenomic data, Whole Genome Sequencing). * non-coding RNA sequence analysis (miRNA, piRNA ...
... reading frames of the capsid and Rep genes along with other representative sequences of circoviruses using Multiple Alignment ... Identifying Distant Circovirus Sequences by Liver Biopsy. Using NGS to analyze viral sequences from the liver biopsy specimen, ... ON677309) and confirmed that the sequence was identical to partial sequences of the capsid gene found in the liver. We ... We performed phylogenetic reconstructions on the capsid protein sequence (Figure 3), on the replicase (Rep) protein sequence ( ...
  • Many MSA tools and genetic alignment algorithms have parameter values either as default or optional making it difficult to select appropriate method and parameter values since the sequence is unknown. (
  • The proposed algorithms select appropriate alignment and parameter values based on sequence length, identity and alignment score, reducing time to optimize parameter values and prevent execution with default values. (
  • Due to the problem of the NP-complete class property, a number of researches use genetic algorithms (GA) to find a solution to the multiple sequence alignment. (
  • 2] Kosmas Karadimitrion and Donald H. Kraft, “Genetic Algorithms and The Multiple Sequence Alignment Problem in Biologyâ€, Proceedings of the Second Annual Molecular Biology and Biotechnology Conference, Baton Rouge, LA., February 1996. (
  • 13] Ben Othman, M.T. ; AbdelÂ- Azim, G., "Multiple sequence alignment based on genetic algorithms with new chromosomes representation", Electro-technical Conference (MELECON) , 2012 16th IEEE Mediterranean, . (
  • What are the main differences in the algorithms of Global and Local alignment? (
  • Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye " prior to phylogenetic inference . (
  • Several researches were conducted to determine the level of similarity of a set of sequences. (
  • How can you define similarity between two protein sequences? (
  • BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (
  • One of the viruses, EMC/2012, has been sequenced, and its sequence similarity to several bat CoVs suggested an animal origin, but a definitive bat species of origin has not yet been identified ( 3 ). (
  • This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (
  • Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (
  • Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (
  • Detecting similarities between (RNA, DNA, and protein) sequences is an important part of bioinformatics. (
  • 11] Naznin, F. ; Sarker , R. ; Essam, D., "DGA: Decomposition with genetic algorithm for multiple sequence alignment", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology ( CIBCB) , 2010, . (
  • Bioinformatics: sequence and genome analysis. (
  • Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (
  • Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (
  • So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (
  • I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (
  • Additional genome sequences from this virus are needed to aid diagnostics, monitor population dynamics, identify the animal source, and characterize mechanisms of pathogenesis. (
  • Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (
  • The third Alignment Reference option is Pairwise . (
  • When Pairwise is selected the Protein Sequence Alignment View will focus on the whole aligned section between Query and Entity sequences displaying all details of the alignment including gaps in both sequences. (
  • Another algorithm (SOSW) performs pairwise alignment and progressively aligns it to a local multiple sequence alignment (MSA) based on the alignment score. (
  • Write a tool that retrieves all Uniprot entries with a given EC number and calculates pairwise sequence similarities. (
  • Compare the species horse ( Equus caballus ), Minke whale ( Balaenoptera acutorostrata ) and Red kangaroo ( Macropus rufus ) based on two of their proteins (do pairwise alignments and compare sequence identities). (
  • alignment but designed for DNA or protein sequences. (
  • Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. (
  • Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods . (
  • To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics . (
  • Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. (
  • Observer agreement for event sequences: Methods and software for sequence alignment and reliability estimates. (
  • Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. (
  • 14] Kumar S, Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. (
  • The alignment of CHROMOSOMES at homologous sequences. (
  • Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (
  • List of commonly used primers detected in a given nucleotide sequence. (
  • We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. (
  • JX869059) were analyzed to identify all possible primer-like sequences (melting temperature 58°C-60°C, guanine plus cytosine content 35%-60%) yielding 357,198 potential primers. (
  • Reverse complements of the 3′ mapping sequences were prepared, resulting in a set of 60 primers for the 15 amplicons (4 primers/amplicon). (
  • ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (
  • Traditionally, sequences are gastroenteritis (AGE) in humans. (
  • A global multiple sequence alignment algorithm (SOGA) includes 2 new operators which perform a self organizing crossover and mutation operation for the required number of generations. (
  • Key Words: Algorithm, sequence alignment. (
  • Sequence Alignment by Genetic Algorithm ", Nucleic Acid Research, Vol. 24, 1515-1524, 1996 . (
  • Batouche, M. , "Multiple sequence alignment by quantum genetic algorithm", 20th International Parallel and Distributed Processing Symposium (IPDPS), 2006, . (
  • 5] Naznin F, Sarker R, Essam D. "Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment. (
  • 6] Naznin, F. ; Sarker , R. ; Essam, D., "Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment", IEEE Transactions on Evolutionary Computation, Vol 16, Issue: 5, . (
  • 7] Pramanik, S. ; Setua, S.K., "A steady state Genetic Algorithm for Multiple Sequence Alignment", International Conference on Advances in Computing, Communications and Informatics (ICACCI), 2014, . (
  • 8] Liu Chao ; Liu Shuai, "The research on DNA multiple sequence alignment based on adaptive immune genetic algorithm", International Conference on Electronics and Optoelectronics (ICEOE) , 2011, Vol 3, . (
  • 12] Miranda, L.A. ; Caetano, M.A.F. ; Melo, A.C.M.A. ; Correa, J.M. ; Bordim, J.L., "Multiple Biological Sequence Alignment with a Parallel Island Injection Genetic Algorithm", 12th IEEE International Conference on High Performance Computing and Communications (HPCC) , 2010, . (
  • Find the best alignment between the sequences "WHAT" and "WHY", using the Needleman-Wunsch algorithm, with +1 for a match, -1 for a mismatch, and -2 for a gap. (
  • Write a small program that calculates a global alignment by implementing the Needleman-Wunsch algorithm and prints out the alignment. (
  • Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. (
  • Web-based to query sequences using a k-mer (DNA substring) based algorithm. (
  • BLAST algorithm against a set of reference sequences followed by notypes [6 ] with viruses in GI, GII, GVIII and GIX infecting humans. (
  • HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (
  • We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. (
  • The full HA and NA genes of 16 H1N1-positive samples obtained in our study and 21 published HA sequences and 20 published NA sequences from Jordanian viruses that were available on online gene databases were analysed. (
  • Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (
  • Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. (
  • The large size (30,000 nt) and high variability of CoV RNA genomes present a challenge for sequencing. (
  • Multiple Sequence Alignment (MSA) is used in genomic analysis, such as the identification of conserved sequence motifs, the estimation of evolutionary divergence between sequences, and the genes’ historical relationships inference. (
  • Increasing the number of sequences from three to seven significantly improved the predictive value of evolutionary computations. (
  • Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. (
  • I did not mean swalign or nwalign, these just for biological sequences. (
  • if not are there anyone wrote a code of sequence alignment for non biological sequences in matlab? (
  • Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (
  • We recommend taking a plurality consensus sequence for each gene segment, genome, and/or lineage/subtype. (
  • The clipper 20 sequence was identical to a subtype D sequence (GenBank accession AY233291) from Gauteng, SA. (
  • selects the base position with the most reads aligned to it, then uses its alignment coverage value for the bin. (
  • Based on the domain architectures and the amino acid sequence homology, the SWIRM domains can be classified into three main types: Swi3/MYSM1 (human MYb-like, Swirm, and Mpn domain-containing protein-1), LSD1 (Lysine-specific demethylase 1), and Ada2 (Adenosine deaminase isoenzymes 2) types [ 13 ]. (
  • All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. (
  • HBV DNA from clipper 16 clustered with genotype A sequences from SA, India, Brazil and Martinique, while clipper 20 clustered with SA genotype D sequences. (
  • We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. (
  • Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. (
  • Venom-peptide research and drug discovery has increased exponentially with the advance of genomic-transcriptomic sequencing and proteomic mass-spectrometry 10 . (
  • RESULTS: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. (
  • A direct genomic approach was implemented in which total DNA from the sample was purified through a column-based method, followed by sequencing on the Nanopore GridION. (
  • 4. Section III, Editing and Interpreting Entries, Guides for the determination of the probability of sequence, Interpretation of "highly improbable", deleted diarrhea and gastroenteritis of infectious origin from the list of infections that may be accepted as "due to" any other disease. (
  • The computational sequence-profile analysis indicates that the typical SWIRM domain consists of 85 amino acid residues and forms a compact helix-turn-helix (HTH)-related structure [ 12 ]. (
  • The sequences were are associated with high morbidity and submitted to GenBank under accession mortality ( 1 ). (
  • The sequence clipboard box will appear with the top strand sequence of the selected region. (
  • and both integers are smaller than the length of the reference sequence. (
  • Column vector of nonnegative integers, each defining the start of a range in the reference sequence. (
  • Column vector of nonnegative integers, each defining the end of a range in the reference sequence. (
  • HA and NA sequences each in the analysis. (
  • Aligned regions are represented using color code blocks that display the sequence identity through a gradient color code. (
  • To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations. (
  • In this case Entity sequences will be used as references. (
  • Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. (
  • It converts a multiple sequence alignment files into an HMM profile. (
  • Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. (
  • To deselect, click back on the nucleotide sequence. (
  • MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. (
  • However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. (
  • Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (
  • Qualimap: evaluating next-generation sequencing alignment data. (
  • MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. (
  • Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. (
  • then only the maximum hit for all reference sequences will be grouped into primary data. (
  • Data from COVID-19 case investigations, contact tracing, the Commonwealth's immunization registry and whole genome sequencing were collated and analysed as part of this study. (
  • Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. (
  • Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (
  • It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (
  • The Protein Sequence Alignment View provides graphical summaries of the aligned regions when a sequence search is performed. (
  • Sarah Gregory] And following on that, what is Next Generation Sequencing? (
  • What does "conservation" mean in the context of sequence alignments? (
  • Despite the small p16 sequence database, our calculations of high conservation correctly predicted loss of cell cycle arrest function in 75% of tested codons, and low conservation correctly predicted wild-type function in 80-90% of codons. (
  • Peu de renseignements sont disponibles sur les mutations des virus saisonniers de la grippe A(H1N1)pdm09 et H3N2 en Jordanie. (
  • Les mutations individuelles sont décrites en détail. (
  • A sequential implementation of Smith-Waterman requires quadratic running time with respect to the length of the sequences. (
  • 10] Al Junid, S.A.M. ; Reffin, M.S. ; Majid, Z.A. ; Tahir , N.M. ; Har on, M.A., "Implementation of genetic algor ithm for optimizing DNA sequence alignment", IEEE Business Engineering and Industrial Applications Colloquium ( BEIAC) , 2012. (
  • The key reform here will be the alignment of the governing bodies' resolutions with corporate priorities, ensuring a more strategic and disciplined approach to decision-making by the Health Assembly, and enabling the necessary oversight of programme and financial implementation, including the fiscal soundness of Organizational practices. (
  • Noroviruses are associated with an compared to an established set of reference sequences to determine estimated 70,000-200,000 deaths annually [2,3 ] while sapoviruses genotypes and polymerase types based on phylogenetic clustering, or by primarily cause sporadic AGE in young children although outbreaks in employing NCBI BLAST web service. (
  • Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (
  • Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus , to compare different alignment approaches. (
  • Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time -intensive than traditional approaches. (
  • Query sequence is used as a reference to display the aligned regions. (
  • The Alignment Reference drop down menu selects the reference that is used to display the aligned regions. (
  • By default the Query option is selected to use the Query sequence as reference. (
  • The Alignment Reference can be changed to Subject . (
  • Nonnegative integer that defines the start of a range in the reference sequence. (
  • Nonnegative integer that defines the end of a range in the reference sequence. (
  • Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (
  • The bottom track displays the aligned regions of the Entity sequence including Entity sequence gaps (or Query sequence insertions) as dashed lines or Entity sequence deletions as white circles in the middle of blocks. (
  • Thank you for your patience as we work to enhance our plasmid and sequence displays. (
  • The Query sequence is displayed in the first track of the Protein Sequence Alignment View. (
  • The first track of the Protein Sequence Alignment View will display the particular Entity sequence excluding any potential gap resulting from the alignment. (
  • Use text editor or plasmid mapping software to view sequence. (
  • Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily- sound groups, regardless of alignment type and support threshold. (
  • Content or materials that correspond with the sequence of learning experiences and help teachers and students meet learning objectives. (

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