Sequence Alignment: 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.Sequence Analysis, Protein: 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Molecular Sequence Data: 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.Computational Biology: 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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Proteins: 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, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Internet: 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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Computing Methodologies: Computer-assisted analysis and processing of problems in a particular area.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Sequence Analysis: 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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Software Validation: The act of testing the software for compliance with a standard.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Word Processing: Text editing and storage functions using computer software.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Markov Chains: 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.Sequence Homology: 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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Protein Structure, Secondary: 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.Computer Graphics: 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.Protein Structure, Tertiary: 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.Databases, Nucleic Acid: 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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Structural Homology, Protein: 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.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Models, Statistical: 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.Databases, Factual: 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.Protein Conformation: 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).Amino Acid Motifs: 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.Models, Genetic: 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.Programming Languages: Specific languages used to prepare computer programs.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)INDEL Mutation: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Sequence Homology, Nucleic Acid: 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.Software Design: Specifications and instructions applied to the software.Entropy: 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)Reproducibility of Results: 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.Cluster Analysis: 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.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Likelihood Functions: 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.Artificial Intelligence: 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.RNA: 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)Cloning, Molecular: 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.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Multigene Family: 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)Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Probability: The study of chance processes or the relative frequency characterizing a chance process.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Quality Control: 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)Archaea: 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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Benchmarking: Method of measuring performance against established standards of best practice.Bacterial Proteins: Proteins found in any species of bacterium.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.DNA: 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).Escherichia coli: 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.Documentation: 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.Sensitivity and Specificity: 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)Bayes Theorem: 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.Genetic Variation: Genotypic differences observed among individuals in a population.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Protein Binding: 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.Mutation: 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.Structure-Activity Relationship: 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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.RNA, Untranslated: 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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.ComputersMonte Carlo Method: 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)Amino Acid Substitution: 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.Species Specificity: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Recombinant Proteins: Proteins prepared by recombinant DNA technology.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Evaluation Studies as Topic: 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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Open Reading Frames: 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).DNA, Complementary: 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.DNA Primers: 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.Polymerase Chain Reaction: 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.Plant 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.Amino Acids: 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.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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Ligands: 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)Membrane Proteins: 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.Cattle: 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.Kinetics: The rate dynamics in chemical or physical systems.DNA, Intergenic: 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.Genome, Human: 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.Exons: 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.Bone Malalignment: Displacement of bones out of line in relation to joints. It may be congenital or traumatic in origin.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Neural Networks (Computer): 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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Codon: 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).Work Simplification: The construction or arrangement of a task so that it may be done with the greatest possible efficiency.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Enzymes: 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.Introns: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genes, Bacterial: The functional hereditary units of BACTERIA.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Sarcocystidae: 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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.
RNA secondary structure prediction from a multiple sequence alignment. Phylogenetic profiling prediction from pairwise present ... CS1 maint: Multiple names: authors list (link) Andre S. Ribeiro; Stuart A. Kauffman; Jason Lloyd-Price; Bjorn Samuelsson & ... Using the ideas of Kolmogorov complexity, one can consider the mutual information of two sequences independent of any ... Strehl, Alexander; Ghosh, Joydeep (2002), "Cluster Ensembles - A Knowledge Reuse Framework for Combining Multiple Partitions" ( ...
Sequence databases: import, maintain, view, and export sequences. Multiple sequence alignment: align sequences of DNA, RNA, or ... and create phylogenetic trees. Sequence alignment software Wright ES (2015). "DECIPHER: harnessing local sequence context to ... improve protein multiple sequence alignment". BMC Bioinformatics. 16: 322. doi:10.1186/s12859-015-0749-z. PMC 4595117 . PMID ... Genome alignment: find and align the syntenic regions of multiple genomes. Oligonucleotide design: primer design for polymerase ...
... on-demand generation of multiple sequence alignments with feature annotations; classification of histone-like sequences and ... The interactive web site supports various searching strategies in both datasets: browsing of phylogenetic trees; ... Baxevanis AD, Landsman D (1996). "Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences". ... Makalowska I, Ferlanti ES, Baxevanis AD, Landsman D (1999). "Histone Sequence Database: sequences, structures, post- ...
The conserved sequence motif 'AUACAAnACCC' was boxed. The phylogenetic tree of sRNA-Xcc1 homologs based on multiple alignments ... Multiple alignment and the consensus secondary structure model of the sRNA-Xcc1 homologs. Multiple alignment was done by using ... ClustalW program and the consensus secondary structure was predicted based on the multiple alignment using RNAalifold program. ...
These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function ... The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on ... The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations ... the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. ...
... the family must contain a high quality sequence alignment. The assessment of multiple aligned sequence is done by assessing a ... Mi, H.; Dong, Q.; Muruganujan, A.; Gaudet, P.; Lewis, S.; Thomas, P.D. (Jan 2010). "PANTHER version 7: improved phylogenetic ... There are a Hidden Markov Model (HMM), a multiple sequence alignment (MSA) and a family tree for each protein family in the ... For each family multiple sequence are aligned using a default setting of MAFFT, any column which is aligned less than 75% of ...
A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree ... It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences ... T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a ... a web server for multiple sequence alignment evaluation and phylogenetic reconstruction". Nucleic Acids Research. 43 (W1): W3-6 ...
One common method is multiple sequence alignment. Cavalier-Smith, G. G. Simpson and Ernst Mayr are some representative ... Molecular systematics uses DNA sequence data for tracking evolutionary changes, thus paraphyly and sometimes phylogenetic ... In phylogenetic nomenclature, there is an added caveat that the ancestral species and all descendants should be included in the ... While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary ...
PANDIT is a database of multiple sequence alignments and phylogenetic trees covering many common protein domains. Phylogeny ... Sequence alignment Whelan, Simon; de Bakker Paul I W; Quevillon Emmanuel; Rodriguez Nicolas; Goldman Nick (Jan 2006). "PANDIT: ...
Multiple sequence alignment algorithms can leave a large amount of indels in the sequence alignment when the indels do not ... If phylogenetic signal of an alignment is too low then a longer alignment or an alignment of another gene in the organism may ... Multiple sequence alignment algorithms (e.g., MUSCLE, MAFFT, and CLUSAL W) will align the data set with all selected sequences ... After the running a multiple sequence alignment algorithm, manual editing the alignment is highly recommended. ...
... for such purposes as multiple sequence alignment (e.g. Clustal and MAFFT), as well as the ability to retrieve DNA sequence data ... Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to MacClade, when ... Stamatakis A (2014). "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies". Bioinformatics ... Mesquite includes some rudimentary tools for phylogenetic tree estimation; however, the Zephyr package provides a Mesquite ...
Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap ... ClustalV: A rewrite of the original Clustal package that included phylogenetic tree reconstruction on the final alignment for ... Multiple Sequence Alignment Methods. Methods in Molecular Biology. Humana Press. pp. 105-116. doi:10.1007/978-1-62703-646-7_6. ... Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003). "Multiple sequence alignment with the ...
Phylogenetic footprinting is a technique that utilizes multiple sequence alignments to determine locations of conserved ... Along with multiple sequence alignments, phylogenetic footprinting also requires statistical rates of conserved and non- ... conserved sequences. Using the information provided by multiple sequence alignments and statistical rates, one can identify the ... In both cases, whether the regulatory sequence occurs before (5') or after (3') the gene it regulates, the sequence is often ...
Progressive sequence alignment methods produce a phylogenetic tree by necessity because they incorporate new sequences into the ... Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction. Nature ... a primary problem is in producing a multiple sequence alignment (MSA) between the genes or amino acid sequences of interest. ... a multiple nucleic acid sequence alignment program". J Heredity. 85: 417-418. Simmons, MP (2004). "Independence of alignment ...
... explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. ... a tool for automated alignment trimming in large-scale phylogenetic analyses". Bioinformatics. 25 (Database issue): 1972-3. doi ... For each sequence, domains and their names are shown, they can be clicked to obtain a short description and the external link ... PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well ...
... is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli ... Output alignments include homology information for sequences at internal nodes of the tree. Sequence alignment software ... BAli-Phy takes alignment uncertainty into account while estimating the phylogeny by averaging over possible alignments. Unlike ... Alignment uncertainty stems from two main sources: near-optimal alignments and evolutionary parameter uncertainty. Evolutionary ...
... visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support ... CS1 maint: Multiple names: authors list (link) Huson, DH; Bryant, D (Feb 2006). "Application of phylogenetic networks in ... Bayesian phylogenetic inference, maximum likelihood and distance matrix methods. List of phylogenetic tree visualization ... Minh, BQ; Nguyen, MAT; von Haeseler, A (May 2013). "Ultrafast Approximation for Phylogenetic Bootstrap". Mol Biol Evol. 30 (5 ...
CS1 maint: Multiple names: authors list (link) Cordes, M. H., Davidson, A. R., and Sauer, R. T (1996). "Sequence space, folding ... CS1 maint: Multiple names: authors list (link) Tatusov RL; et al. (2001). "The COG database: new developments in phylogenetic ... SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268-272. doi:10.1093/nar/30.1.268. ... Nature is a tinkerer and not an inventor, new sequences are adapted from pre-existing sequences rather than invented. Domains ...
... is a multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence ... and the phylogenetic analysis tool Xrate. A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm ... GF Above the alignment #=GC Below the alignment #=GS Above the alignment or just below the corresponding sequence #=GR Just ... Do not use multiple lines with the same #=GC label. For a single sequence, do not use multiple lines with the same #=GR label. ...
Analyses currently supported include multiple sequence alignments, construction of phylogenetic trees, motif searches and scans ... KEGG Multiple Sequence Alignment MicrobesOnline home page IMG home page reference: Nucleic Acids Research, 2006, Vol. 34, ... NCBI Taxonomy is used to classify the species and sequences into phylogenetic groups, and build a phylogenetic tree. ... For the sequence search tool, MicrobesOnline integrates BLAT, FastHMM and FastBLAST to search protein sequences, and uses ...
... such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored ... and annotate nucleic acid and protein sequences Fast search in a sequence Multiple sequence alignment: Clustal W and O, MUSCLE ... Sequences and annotations: FASTA (.fa), GenBank (.gb), EMBL (.emb), GFF (.gff) Multiple sequence alignments: Clustal (.aln), ... editing the alignment, analyzing it, storing the consensus sequence, building a phylogenetic tree, and so on. The Phylogenetic ...
... whole-genome pairwise and multiple alignment editor. The program highlights differences between consecutive pairs of sequences ... Additional analysis tools such as BLAST searches, genome maps, genome or gene alignment, phylogenetic trees, etc. are provided ... VGO can also be used to identify related genes across multiple sequences. BBB (Base-by-Base) Base-By-Base is a platform- ... Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it also generates ...
It is used to discover patterns of evolutionary conservation in sequence alignments. The program can be used to estimate ... These varying pressures show up clearly in multiple alignments. The sequential layout of introns and exons can be described ... Westesson, O.; Holmes, I. (2012). "Developing and applying heterogeneous phylogenetic models with XRate". PLoS One. 7. doi: ... The program allows specification of a variety of models of DNA sequence evolution which may be arbitrarily organized using ...
Furthermore, cTFbase also provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding ... including sequence features, domain architecture and sequence similarity against the linked databases. ... PCC6803 genome and created a consensus RBS sequence (TAGTGGAGGT), which had 5 times higher output than the consensus E. coli ... In order to create plasmids-stable, replicating circular pieces of DNA-that will function successfully in multiple species, a ...
... has a wide range of functions in addition to multiple sequence alignment viewing and editing including calculating phylogenetic ... Jalview is a piece of bioinformatics software that is used to look at and edit multiple sequence alignments. It is written in ... Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (May 2009). "Jalview Version 2--a multiple sequence alignment editor ... "Release History". Clamp M, Cuff J, Searle SM, Barton GJ (February 2004). "The Jalview Java alignment editor". Bioinformatics. ...
1999, 2nd 2002]. Plant systematics: a phylogenetic approach (3rd ed.). Sinauer Associates. ISBN 978-0-87893-407-2. .. ... There is a regularity in these angles and they follow the numbers in a Fibonacci sequence: 1/2, 2/3, 3/5, 5/8, 8/13, 13/21, 21/ ... However, horizontal alignment maximizes exposure to bending forces and failure from stresses such as wind, snow, hail, falling ... However, these simplified systems allow for further division into multiple subtypes. Simpson, (and others) divides ...
... multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments. For ... Sequence Read Archive (SRA) The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing ... A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding ... while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms. ...
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree ... T-Coffee; alignment confidence; alignment uncertainty; homology modeling; multiple sequence alignment; phylogeny ... Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary ... We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data ...
sequence extraction from phylogenetic trees How to extract multiple sequences in FASTA format from a phylogenetic tree image in ... Multiple sequence alignment and phylogenetic analysis Hi, I have a theoretical question that puzzles me: When I am doing an MSA ... Multiple-Sequence Alignment Trimming I want to construct a phylogenetic tree based on 5 housekeeping loci from two different ... Effective Scoring Function To Compare Multiple Sequence Alignments Or Phylogenetic Trees I am wondering if there is any good ...
Phylogenetic use. Multiple sequence alignments can be used to create a phylogenetic tree. This is made possible by ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments". BMC ... Multiple sequence alignment also refers to the process of aligning such a sequence set. Because three or more sequences of ...
... since they may not be homologous or may have been saturated by multiple substitutions. A computerize … ... The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, ... The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, ... Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol Biol Evol. 2000 Apr;17(4):540 ...
Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned ... Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. ... if several alignments for the same set of sequences are provided, the level of consistency across different alignments. ... trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.. Capella-Gutiérrez S1, Silla-Martínez JM ...
Multiple sequence alignment was performed by Muscle alignment using MEGA740. The evolutionary history was inferred by using the ... Sequence alignment and phylogenetic tree. Protein homology searches for MHETase-like proteins were performed with the NCBI ... The nucleotide sequence was confirmed by sequencing at Eurofins (Ebersberg, Germany).. Autohydrolysis of MpNPT. Hydrolysis was ... Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403- ...
Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-speciﬁc ... T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217. Nye, T.M., Lio, P., ... 2.6.1. Phylogenetic reconstruction and comparison We used sequence alignments separately to obtain individual trees, under both ... Phylogenetic analysis of Penicillium species based on ITS and LSU-rDNA nucleotide sequences. In: Samson, R.A., Pitt, J.I. (Eds ...
In this study, we considered the most important polyketide and peptide mycotoxins and, for the first time, a phylogenetic ... Hybrid PKS-NRPSs involved in mycotoxins biosynthesis grouped together in the phylogenetic trees of all the domains analyzed. ... Multiple Sequence Alignment and Phylogenetic Analysis. The reconstruction of a good and reliable phylogenetic tree is crucially ... Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797 ...
Phylogenetic tree and sequence similarities suggested OsCCR4, 5, 17, 18, 19, 20, and 21 as likely candidates for functional ... Phylogenetic tree and sequence similarities suggested OsCCR4, 5, 17, 18, 19, 20, and 21 as likely candidates for functional ... Phylogenetic analysis revealed that OsCCR19 and 20 were grouped with other plant CCRs involved in developmental lignification, ... In agreement with the phylogenetic analysis, expression analysis demonstrated that OsCCR20 was constitutively expressed ...
How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in ... What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem? ... What does it mean to not be able to take the derivative of a function multiple times? ... What is the best argument for maximum parsimony method in phylogenetic tree construction? ...
... and classified them into 12 distinct subfamilies based upon their sequence composition and phylogenetic positions. To further ... and classified them into 12 distinct subfamilies based upon their sequence composition and phylogenetic positions. To further ... phylogenetic tree, tissue expression patterns of the 189 AAT genes in soybean. We found that a large number of AAT genes in ... phylogenetic tree, tissue expression patterns of the 189 AAT genes in soybean. We found that a large number of AAT genes in ...
Alignment and phylogenetic analysis of MYB-related TFs. Multiple alignment of the amino acid sequences was performed via ... Phylogenetic tree analysis with amino acid sequence of 139 MYB-related genes. Alignment of the amino acid sequences was used to ... 2, the phylogenetic tree was divided into 5 groups (I-V). The sequence SHAQK(Y/F) F was highly conserved in group I. Group II ... Phylogenetic tree of the MYB-related TFs subfamily in soybean. Amino acid sequences were aligned via ClustalX and were manually ...
Multiple Sequence Alignments and Phylogenetic Analysis. Multiple sequence alignments of related proteins belonging to each ... B, Alignment of putative DNA-binding motifs of B-type RRs. Multiple sequence alignment was done using T-Coffee software. C, ... Deduced multiple sequence alignment of putative RR and PRR proteins in O. sativa. A, Amino acid sequences of transmitter ... Amino acid sequence alignment of HK transmitter (A) and RDs and related proteins (B) in O. sativa. Sequence alignment was done ...
RNA secondary structure prediction from a multiple sequence alignment. Phylogenetic profiling prediction from pairwise present ... CS1 maint: Multiple names: authors list (link) Andre S. Ribeiro; Stuart A. Kauffman; Jason Lloyd-Price; Bjorn Samuelsson & ... Using the ideas of Kolmogorov complexity, one can consider the mutual information of two sequences independent of any ... Strehl, Alexander; Ghosh, Joydeep (2002), "Cluster Ensembles - A Knowledge Reuse Framework for Combining Multiple Partitions" ( ...
The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction. Lebrun E, ... The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction March 28, 2006 ... Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske ... Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, ...
Sequence Identification, Multiple Sequence Alignments, and Phylogenetic Analysis. DNA sequences were edited and assembled using ... Phylogenetic comparison of the sequences of the full-length cDNAs with other related sequences assigned SrCPS2 and SrKSL to the ... 2015) Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci USA 112: E81-E88. ... An SsLPPS sequence was detected by deep 454 sequencing of cDNAs from clary sage (Salvia sclarea) calices, where sclareol, a ...
On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for ... detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence ... The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic ... analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with ...
Abstract Background The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic ... that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. For each ... a new software for selection of phylogenetic informative regions from multiple sequence alignments. ... Conclusions BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid ...
Alignment of 1.4 million sequences is made possible by upgrading T-Coffee with a regressive alignment algorithm. ... Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from ... It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their ... We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially ...
Pretty-printing of multiple sequence alignments. bppphyview (0.3.0-1). Bio++ Phylogenetic Viewer. bwa (0.7.10-1). Burrows- ... Segment-based multiple sequence alignment. dialign-tx (1.0.2-7). Segment-based multiple sequence alignment. dialign-tx-data ( ... Efficient sequence alignment of full genomes. muscle (1:3.8.31-1). Multiple alignment program of protein sequences. music-bin ( ... multiple sequence alignment editor. acedb-other-dotter (4.9.39+dfsg.01-5). visualisation of sequence similarity. aces3 (3.0.8-4 ...
... multiple sequence alignment; functional-characterization; phylogenetic analysis; transport-system; binding-protein; fungal ... genomes; reticuli; soil; cellulases; streptomyces; cellulose; plant genomics; evolutionary genetics; gene expression; sequence ...
Multiple sequence alignment. *Phylogenetic tree inference. *Phylogenomics. *Genome-scale index structures (suffix trees, ... Sequence alignment: General overview. Slides (full), Slides (handout) 3. Sequence alignment: Scoring schemes. Slides (full), ... Profiles and multiple sequence alignments. Slides (full), Slides (handout). 9. Phylogenetics: Recovering Evolutionary History. ... Sequence alignment: Dynamic programming algorithms for pairwise alignment. Slides (full), Slides (handout). ...
Phylogenetic Analysis Multiple Sequence Alignment Novel Graph-Theoretical Based Genomic Models Computational Methods for Probe ... as well as in sequencing DNA, and identifying protein structures. Optimization in Medicine and Biology provides researchers ...
Here, we combine genomic and transcriptomic sequence data from vertebrate organisms to study the evolution of periostin and ... Multiple sequence alignments and phylogenetic trees. All multiple sequence alignments were performed using the ClustalW ... Phylogenetic trees based on alignments of periostin sequences. (A) The phylogenetic tree obtained from a protein sequence ... Prediction results are shown in Figure 3 in the context of a multiple sequence alignment of the nine sequences.. ...
GenBankAnnotationOrganismBuilding phylogenetic treesInferenceGenomesBioinformaticsGeneGenesSpeciesReconstructionFastaDistantly relatedStructuralConstruction of phylogeneticEvolutionary HistoryDatasetsCLUSTALEvolutionMSAsConstructComputationalProtein alignmentsAlgorithmsGenome SequencingPairs of sequencesPhylogeniesSimilaritiesInsertionsAccurate Multiple SequenceNucleotide or amino acidAmino Acid SeqHomologousProgressivePairwise alignmentGeneticSamples sequencedViralGlobal alignmentUncertaintyMotif
- A divison of GenBank that contains short single-pass reads of cDNA (transcript) sequences. (unt.edu)
- GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. (unt.edu)
- A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank. (unt.edu)
- It provides tools for flu sequence analysis, annotation and submission to GenBank. (unt.edu)
- A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. (unt.edu)
- This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases. (unt.edu)
- Abstract Background The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. (journaldatabase.info)
- Results Here is presented a new software, named BMGE (Block Mapping and Gathering with Entropy), that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. (journaldatabase.info)
- Sets of contiguous characters with a score above a given threshold are considered as not suited for phylogenetic inference and then removed. (journaldatabase.info)
- Ogden TH, Rosenberg MS (2006) Multiple sequence alignment accuracy and phylogenetic inference. (springer.com)
- All isolates except that from North-Central India formed a distinct phylogenetic clade, notwithstanding low bootstrap support and collapse of the clade in Bayesian Inference. (hindawi.com)
- Sequence alignment and inference of the phylogenies is a standard procedure for analyzing biological sequences. (biomedcentral.com)
- Phylogenetic Inference: 4. (cambridge.org)
- These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines. (blogspot.com)
- Molecular evolutionary phylogenetic inference ( pdf ) ( Lab Report #8 ). (fsu.edu)
- How to use PAUP* (Phylogenetic Analysis Using Parsimony [and Other Methods], PHYLIP (PHYLogeny Inference Package), and other tools to ascertain and draw phylogenetic trees from multiple sequence alignment datasets. (fsu.edu)
- Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. (els.net)
- To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. (nih.gov)
- A current scientific trend is to build phylogenetic trees from a large number of sequence datasets (semi-)automatically extracted from numerous complete genomes. (journaldatabase.info)
- While Löytynoja and Goldman didn't explicitly write how their new algorithim, described in, " Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis ," impacts our understanding of human evolution and how we compare primate genomes, it is an important to understand what they've accomplished. (anthropology.net)
- Up until now, people compared and contrasted sequencing similarities of multiple genomes using a tool that does a multiple sequence alignment. (anthropology.net)
- Since the discovery of transposable elements (TEs) in corn [ 1 ], DNA sequencing has revealed that genomes of eukaryotic organisms are largely comprised of evolutionarily significant TEs responsible for creation of considerable genetic diversity [ 2 ]. (hindawi.com)
- Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. (plos.org)
- Low to medium density pear genetic maps enriched with apple microsatellite markers have enabled the alignment of genetic maps of European pear and apple and formulation of the hypothesis that apple and pear have collinear genomes - . (plos.org)
- Although this hypothesis was based on few hundred orthologous markers only, the recent comparison of several sequenced rosaceous genomes indicates that even among the more distantly related genomes of apple, peach and strawberry , , synteny is conserved. (plos.org)
- This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. (geometry.net)
- As more species' genomes are sequenced, computational analysis of these data has become increasingly important. (cshlpress.com)
- Multiple sequence alignments are central to many areas of bioinformatics. (nih.gov)
- In bioinformatics , a sequence alignment is a way of arranging the sequences of DNA , RNA , or protein to identify regions of similarity that may be a consequence of functional, structural , or evolutionary relationships between the sequences. (wikipedia.org)
- Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. (routledge.com)
- The multiple alignments were generated using multiz and other tools in the UCSC/ Penn State Bioinformatics comparative genomics alignment pipeline. (ucsc.edu)
- To reinforce the theory underlying the concepts and techniques of sequence analysis and post-genomic bioinformatics. (ncl.ac.uk)
- Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins is fully referenced and provides appendices, sample sequence file formats, and over 120 illustrations. (abebooks.co.uk)
- A must have for molecular biologists, geneticists, and any biologist interested in genes and proteins, it can also be used in a one-semester practical course on sequence analysis and bioinformatics. (abebooks.co.uk)
- Bioinformatics For Dummies will show you how to get the most out of your PC and the right Web tools so you'll be searching databases and analyzing sequences like a pro! (geometry.net)
- Click here to view the growing list of universities adopting Bioinformatics: Sequence and Genome Analysis, Second Edition for course use. (cshlpress.com)
- New chapters in this second edition cover statistical analysis of sequence alignments, computer programming for bioinformatics, and data management and mining. (cshlpress.com)
- In conclusion, the second edition of Bioinformatics: Sequence and Genome Analysis is an excellent textbook for bioinformatics introductory courses for both life sciences and computer science students, and a good reference for current problems in the field and the tools and methods employed in their solution. (cshlpress.com)
- Recognizing the ever-expanding contributions that next-generation sequencing (NGS) experiments are making to public health and the biological sciences, the Bioinformatics Core provides broad analysis of NGS data. (wadsworth.org)
- I have used muscle (3.8) to perform a multiple sequence alignment on 635 tumor suppressor gene sequences and edited (via perl) the output file so it conforms with FASTA. (biostars.org)
- To further investigate the functions of these genes, we analyzed the chromosome distributions, gene structures, duplication patterns, phylogenetic tree, tissue expression patterns of the 189 AAT genes in soybean. (frontiersin.org)
- A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. (biomedcentral.com)
- Although conventional approaches, such as sequencing of 16SRNA gene, have provided useful information on population structure among the Borrelia spp. (cdc.gov)
- The phylogenetic analysis and expression profiles of tomato P450 gene family offers essential genomic resource for their functional characterization. (springer.com)
- In the present study genetic heterogeneity in the porB genes of N. gonorrhoeae was examined, and serovar determination was compared to porB gene sequencing. (asm.org)
- When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. (biomedcentral.com)
- The central DNA transposase gene encodes, in eight exons, a predicted 160-KDa protein producing BLAST alignments with En/Spm -type transposons. (hindawi.com)
- We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. (pnas.org)
- We align each set of the gene sequences by means of a progressive multiple-sequence alignment algorithm, using the clustalw computer program ( 12 ), with corrections made by eye. (pnas.org)
- We perform the phylogenetic analysis of the Dhfr gene by using the branch-and-bound search method with maximum parsimony optimization criterion of paup ( 14 ). (pnas.org)
- This trend is supported by the increasing demand for sequencing platforms with increasing life science research using techniques such as gene expression analysis, sequence analysis, and protein expression analysis. (bio-medicine.org)
- For the characterization of genetic heterogeneity in this species, the homologue of Anaplasma marginale major surface protein 4 gene ( msp4 ) was identified, and the coding region was PCR amplified and sequenced from a variety of sources, including 50 samples from the United States, Germany, Poland, Norway, Italy, and Switzerland and 4 samples of A. phagocytophilum -like organisms obtained from white-tailed deer in the United States. (asm.org)
- The sequence analysis of the recently discovered A. phagocytophilum msp2 gene corroborated these results. (asm.org)
- Therefore, for the first time we can empirically evaluate gene pleiotropy from the protein sequence analysis. (genetics.org)
- The principle behind our present work in modeling protein sequence evolution is as follows: First, multifunctionality of a gene (pleiotropy) is characterized by K distinct components in the fitness (called molecular phenotypes ). (genetics.org)
- Case studies of vertebrate proteins demonstrate that for the first time we can empirically evaluate gene pleiotropy only from phylogenetic sequence analysis. (genetics.org)
- Pleiotropy of a gene (protein) function can be modeled by multiple ( K ) molecular phenotypes, denoted by ( y 1 , …, y K ). Each molecular phenotype y i represents a nontrivial component of genetic variation, contrasting with organismal fitness as a result of a specific (yet unknown) biological process ( Figure 1 ). (genetics.org)
- If you will not find any from the above then retrieve any five organisms having this gene sequence. (assignmentexpert.com)
- ium solani species complex based on phylogenetic spe- cies recognition on ITS, partial RPB2 and EF-1α gene Keywords Fusarium solani species complex fragments. (deepdyve.com)
- An alignment of a portion of the γ‐fibrinogen gene sequence from five mammals. (els.net)
- I have amino acid sequences of about 900 genes from 20 species and I want to construct a phylogen. (biostars.org)
- We sequenced mating type (MAT) genes and nuclear DNA fragments in sexual and putatively asexual species. (scribd.com)
- In this study, we identified 189 AAT genes from the entire soybean genomic sequence, and classified them into 12 distinct subfamilies based upon their sequence composition and phylogenetic positions. (frontiersin.org)
- Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. (plantphysiol.org)
- We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine ( Vitis vinifera ), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. (biomedcentral.com)
- On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants. (biomedcentral.com)
- The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes. (biomedcentral.com)
- Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. (springer.com)
- Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. (springer.com)
- Recombination signal (RS) sequences flank the variable (V), diversity (D), and joining (J) genes of these loci and allow these genes to be recombined within B or T cells in order to generate the diversity and pattern recognition ability of their surface receptors. (springer.com)
- Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. (pnas.org)
- This report would enable researchers working on Tomato P450 to select appropriate candidate genes from huge repertoire of P450 genes depending on their phylogenetic class, tissue specific expression and promoter prevalence. (springer.com)
- Finally, we found that 10 of the 19 miR828-targeted MYB s undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. (biomedcentral.com)
- We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family. (biomedcentral.com)
- Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. (biomedcentral.com)
- Assessment of DNA sequence variation has been based almost exclusively on examination of several genes coding for antigenic determinants, where amino acid polymorphisms (nonsynonymous nucleotide polymorphisms) are common and likely to be affected by natural selection ( 6 , 7 ). (pnas.org)
- Analysis of finished and unfinished genome sequences showed that some nondenitrifying pathogens have the genes for qNor, suggesting that the enzyme plays a role in escaping host defense by detoxification of NO. Flavohemoglobin, which has NO dioxygenase (NOD) activity under aerobic conditions and NOR activity under anaerobic conditions, is also known to be involved in detoxification of NO ( 42 ). (asm.org)
- The analysis of the structure, organization, phylogeny, and distribution of ask and hom genes revealed that the presence of multiple copies of these genes and their fusion events are restricted to the γ-subdivision of proteobacteria. (biomedcentral.com)
- Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome. (blogspot.com)
- If we find out these specific genes from NCBI within five different species then we are able to find out their respective protein sequences and it would be quite easy to discover the conservation of these proteins among different organisms. (assignmentexpert.com)
- How to design and analyze oligonucleotide primers for discovering genes in organisms where they have not been identified when the gene's encoded protein sequence is known in other organisms. (fsu.edu)
- At the same time we carried out phylogenetic analysis for this genes. (biomedcentral.com)
- There are many different ways to align the genes such as multiple or arranged in parts. (coursehero.com)
- To solve this our tool automatically invokes information about the corresponding sequences in closely related species, such as gorilla or macaque. (anthropology.net)
- Determining which of the vast amounts of sequence differences that are found among individuals of a species contribute to heritable traits will allow diseases to be tackled at the molecular level and aid in the development of novel therapies. (pnas.org)
- The protein is comprised of both an extracellular domain that is highly conserved between insect and vertebrate species, and an intracellular domain for which there is little sequence similarity between the insects and vertebrates. (biomedcentral.com)
- Based on the reconstructed phylogenetic relationship, the evolutionary histories of sampled species, individuals, or strains can be inferred. (biomedcentral.com)
- This track shows multiple alignments of 100 vertebrate species and measurements of evolutionary conservation using two methods ( phastCons and phyloP ) from the PHAST package , for all species. (ucsc.edu)
- We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. (plos.org)
- The population structure of L . calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. (plos.org)
- In addition, population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals representing diverse geographic locations stretching from North-Western India across South-East Asia and Australia to Papua New Guinea. (plos.org)
- a list of names (such as species or products), to label the leaf nodes in the phylogenetic tree object. (mathworks.com)
- Multiple sequence alignment of γD-crystallin protein in different species. (molvis.org)
- Nowadays, subdivisions within Fu- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands sariumaremadeinspeciescomplexesconsistingofsibling species with limited to no morphological variation, which A. D. van Diepeningen (*) can be best discriminated based on sequence data. (deepdyve.com)
- By modelling patterns of molecular change in protein and deoxyribonucleic acid (DNA) sequences over time, scientists now routinely reconstruct evolutionary histories of species and evaluate confidence levels of the inferences. (els.net)
- TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. (nih.gov)
- We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. (nih.gov)
- It has been shown that removing ambiguously aligned regions, but also other sources of bias such as highly variable (saturated) characters, can improve the overall performance of many phylogenetic reconstruction methods. (journaldatabase.info)
- Holmes IH (2017) Historian: accurate reconstruction of ancestral sequences and evolutionary rates. (springer.com)
- Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. (pubmedcentralcanada.ca)
- So the way I see the two programs working together is 1) Zorro discovers regions with low alignment support and then 2) picsord converts these regions to pseudo-characters to aid reconstruction. (blogspot.com)
- How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format? (stackexchange.com)
- The initial guide tree is determined by an efficient clustering method such as neighbor-joining or UPGMA, and may use distances based on the number of identical two letter sub-sequences (as in FASTA rather than a dynamic programming alignment). (wikipedia.org)
- W.R. Pearson , Rapid and Sensitive Sequence Comparison with FASTP and FASTA. (elsevier.com)
- Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. (wikipedia.org)
- Performance is also particularly bad when all of the sequences in the set are rather distantly related. (wikipedia.org)
- Due to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. (pubmedcentralcanada.ca)
- We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees. (nih.gov)
- A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. (wordpress.com)
- In order to integrate structural information into sequence-based evolutionary models, we recently developed a stochastic model of structural evolution on a phylogenetic tree and implemented this as the StructAlign plugin for the StatAlign statistical alignment package. (springer.com)
- The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. (wikipedia.org)
- Gotoh O (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. (els.net)
- Internet sequence and structural databases as well a brief introduction to the Wisconsin Package ( aka Genetics Computer Group or GCG) and its graphical user interface (GUI) SeqLab and the on-site GCG sequence databases will be reviewed. (fsu.edu)
- Identification of domains under low sequence identity conditions and lack of structural homologues acquire a crucial importance especially at the genomic scale. (pubmedcentralcanada.ca)
- Hogeweg, P. & Hesper, B. The alignment of sets of sequences and the construction of phylogenetic trees. (nature.com)
- Our work in this area was originally focused on developing methods for inferring unrooted phylogenetic networks and our computer program, SplitsTree, is currently the most widely-used software for the construction of phylogenetic networks. (uni-tuebingen.de)
- The sequence of YJM789 has implications for the functional significance of genetic variation during pathogenicity, its evolutionary history, and the development of new approaches that determine the contribution of allelic variants to phenotypes. (pnas.org)
- The major problem is that finding the most accurate alignment parameters in progressive and consistency based alignment approaches is difficult due to the incomplete knowledge of the evolutionary history of sequences and/or heterogeneous processes along sequences [ 6 ]. (pubmedcentralcanada.ca)
- The evolutionary history of TMEM18 was inferred using phylogenetic and bioinformatic methods. (biomedcentral.com)
- TreeBASE stores phylogenetic trees and datasets. (bio.net)
- We used the HOMFAM protein sequences dataset to show that on datasets larger than 100 sequences, this instability affects on average 21.5% of the aligned residues. (pasteur.fr)
- Compared with the regular bootstrap procedure, unistrap provides branch support estimates that take into account a larger fraction of the parameters impacting tree instability when processing datasets containing a large number of sequences. (pasteur.fr)
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. (nature.com)
- CLUSTAL will take long strings of DNA sequences and align them based upon their shared similarities. (anthropology.net)
- These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of.50 sequences. (psu.edu)
- The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. (psu.edu)
- Higgins DG, Thompson JD and Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. (els.net)
- We studied the mode of reproduction and its evolution in the fungal subgenus Penicillium Biverticillium using phylogenetic and experimental approaches. (scribd.com)
- While there exist well-studied models of sequence evolution, structurally informed alignment methods have typically made use of geometric measures of deviation that do not take into account the underlying mutational processes. (springer.com)
- We present a method that combines the strengths of tree- and profile-based alignment algorithms and simultaneously describes the evolution and regional heterogeneity, from here on called sequence structure , of multiple sequences. (royalsocietypublishing.org)
- In their sample set, they compared sequences of primates to primates, primates to rodents, and primates to all mammals, they were able to identify that insertions are far more common in primate evolution than deletions. (anthropology.net)
- Here, we combine genomic and transcriptomic sequence data from vertebrate organisms to study the evolution of periostin and particularly of its C-terminal region. (biomedcentral.com)
- Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements. (pubmedcentralcanada.ca)
- Multiple alignment is a powerful integrative tool that addresses a variety of biological problems, ranging from key functional residue detection to the evolution of a protein family. (els.net)
- In this article, we develop an evolutionary model for protein sequence evolution. (genetics.org)
- It is desirable to develop a novel framework that can provide an integrated view of protein evolution, but an unsolved key problem is how to deal with the sophisticated relationship between protein sequence and organismal fitness. (genetics.org)
- This alignment process is being applied to many other areas of molecular phylogenetic and evolution. (coursehero.com)
- 1.1 Alignment and Evolution. (wiley.com)
- MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex . (wikipedia.org)
- The resulting Maximum Likelihood (ML) trees estimated from these MSAs are equally unstable with over 38% of the branches being sensitive to the sequence input order. (pasteur.fr)
- Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. (uni-wuerzburg.de)
- Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. (wikipedia.org)
- A variety of computational algorithms have been applied to the sequence alignment problem. (wikipedia.org)
- This textbook, by one of the leaders of the field (Daniel Huson) and his co-authors, provides a mathematically rigorous introduction to one of the most exciting and beautiful research areas in computational biology: phylogenetic networks. (uni-tuebingen.de)
- Therefore, how to design efficient tools for biologists to analyze and visualize alignments of many sequences has become a challenge for computational biologists. (biomedcentral.com)
- Presented by leading authorities in computational biology, this edited volume covers the gamut of topics, from using software and Internet resources to submitting DNA sequences to databases. (abebooks.co.uk)
- however, the recent application of various new computational techniques to the multiple alignment problem has led to a number of interesting new developments. (els.net)
- Experimental and/or computational methods can be used to identify domains in the given protein sequence. (pubmedcentralcanada.ca)
- In protein alignments, such as the one in the image above, color is often used to indicate amino acid properties to aid in judging the conservation of a given amino acid substitution. (wikipedia.org)
- Besides this information-theoretical advantage, protein alignments also benefit from the information that is implicit in empirical substitution matrices such as BLOSUM-62. (nih.gov)
- RevTrans also accepts user-provided protein alignments for greater control of the alignment process. (nih.gov)
- Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). (wikipedia.org)
- The Tubingen group has led the development of phylogenetic network algorithms, and this book delivers a clear exposition for biologists bewildered by a plethora of recent methods, as well as for bioinformaticians aiming to develop the field further. (uni-tuebingen.de)
- S. Henikoff, J.C. Wallace, and J.P. Brown , Finding Protein Similarities with Nucleotide Sequence Databases. (elsevier.com)
- J.F. Collins and A.F.W. Coulson , Significance of Protein Sequence Similarities. (elsevier.com)
- Identification of domains at the sequence level depends on the detection of global and local sequence similarities between a given query sequence and domain sequences found in databases such as Pfam[ 5 ]. (pubmedcentralcanada.ca)
- We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. (royalsocietypublishing.org)
- This is complicated by base substitutions that decrease similarity between sequences over evolutionary time and insertions and deletions that add and remove sequence in different evolutionary lineages. (royalsocietypublishing.org)
- In addition, information from closely related sequences can be used to infer sites as "permanent" insertions that cannot be matched in subsequent alignments, so that distinct insertion events are correctly kept separate even when they occur at exactly the same position. (anthropology.net)
- Globally high divergence at the sequence level has been inferred from genetic crosses ( 19 ), from sequencing portions of its genome ( 1 , 25 ), and from hybridization to oligonucleotide arrays that could detect the presence of SNPs and insertions/deletions (indels) but not their sequence identity ( 1 , 25 - 28 ). (pnas.org)
- This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. (royalsocietypublishing.org)
- Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix . (wikipedia.org)
- the consensus sequence is also often represented in graphical format with a sequence logo in which the size of each nucleotide or amino acid letter corresponds to its degree of conservation. (wikipedia.org)
- The model predicts eight surface-exposed loops, which exhibit an extensive variation in length and amino acid sequence and which are interspaced with nine more conserved predominantly transmembrane regions (referred to as interspacing regions in the text below). (asm.org)
- Except for a stop signal, another ORF encodes a Ty1-copia -like reverse transcriptase with amino acid sequence domain YVDDIIL. (hindawi.com)
- Sequence alignment aims to match homologous characters, nucleotides or amino acids that are descended from a common ancestor. (royalsocietypublishing.org)
- Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. (biomedcentral.com)
- With Phylo-mLogo , the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. (biomedcentral.com)
- Kumar S and Filipski A (2007) Multiple sequence alignment: in pursuit of homologous DNA positions. (els.net)
- Progressive alignments are not guaranteed to be globally optimal. (wikipedia.org)
- Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. (wikipedia.org)
- We show that all currently available large-scale progressive multiple alignment methods are numerically unstable when dealing with amino-acid sequences. (pasteur.fr)
- The basic progressive alignment procedure, exemplified by a set of five immunoglobulin‐like domains. (els.net)
- Feng DF and Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. (els.net)
- Our approach is based on a pairwise alignment model that consists of a moderate number of evolutionary processes, each describing a set of differently evolving sequence sites or a sequence region. (royalsocietypublishing.org)
- The new version (5.3) of MAFFT offers new iterative refinement opti-ons, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. (psu.edu)
- The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits. (pnas.org)
- however, DNA sequence-based genetic diversity of this aromatic herb is not yet known. (hindawi.com)
- BIOL 5381 Genomics (3 semester hours) The fundamentals of how the human genome sequence was acquired and the impact of the human genome era on biomedical research, medical care and genetic testing will be explored. (utdallas.edu)
- In our study, we employed long read sequencing combined with genetic and optical mapping, and syntenic information to produce a chromosomal level assembly. (plos.org)
- Pak-choi is an important Brassica crop with exceptional cold resistance [ 31 ], and its nearest genetic relative that has been sequenced is Chinese cabbage ( B. rapa ssp. (biomedcentral.com)
- The core's efforts are primarily focused on prokaryotic and viral sequences. (wadsworth.org)
- Specific primers based on the sequence of a previously characterized PLYV isolate were used for the RT-PCR-based amplification of a 900 bp fragment corresponding to the central region of the viral genome. (scielo.br)
- Fragments from 21 viral isolates were cloned and sequenced. (scielo.br)
- Sela I, Ashkenazy H, Katoh K, Pupko T (2015) GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. (springer.com)
- Herman JL, Novák Á, Lyngsø R, Szabó A, Miklós I, Hein J (2015) Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. (springer.com)
- A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. (blogspot.com)
- Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. (blogspot.com)
- Also, there is an alignment uncertainty symposium at SMBE in Dublin this year. (blogspot.com)
- The conserved sequence motif 'AUACAAnACCC' was boxed. (wikipedia.org)
- Outside apparent LTRs, an 8-mer nucleotide sequence motif CACTATAA, near or within inverted repeat sequences, is hypothetical extreme termini. (hindawi.com)
- We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. (uni-wuerzburg.de)