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Sequence alignment

Index Sequence alignment

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. [1]

115 relations: Accelrys, Active site, Additive smoothing, Alignment-free sequence analysis, Alternative splicing, Amino acid, Benchmark (computing), Bioinformatics, Biomolecular structure, BioPerl, Biopython, BioRuby, BLAST, BLOSUM, Bowtie (sequence analysis), Burrows–Wheeler transform, CATH database, Clustal, Coalescent theory, Comparative method, Computer memory, Consensus sequence, Conserved sequence, Contig, Convergent evolution, Data set, Desmond G. Higgins, Distance matrix, DNA, DNA repair, DNASTAR, Dot plot (bioinformatics), Dynamic programming, Edit distance, EMBOSS, Enzyme, Evolution, Expressed sequence tag, Families of Structurally Similar Proteins database, FASTA, FASTA format, FM-index, Gap penalty, GenBank, Gene, Genetic algorithm, Genetic code, Genome, Global optimization, Hemagglutinin, ..., Heuristic, Heuristic (computer science), Hidden Markov model, Human, Hydrophobe, Indel, Inverted repeat, Linguistics, List of sequence alignment software, Loss function, Main diagonal, Margaret Oakley Dayhoff, Mathematical optimization, Matrix (mathematics), Molecular clock, Most recent common ancestor, Multiple sequence alignment, Natural language, Natural language processing, Natural selection, Needleman–Wunsch algorithm, NP-completeness, NP-hardness, Nuclear magnetic resonance spectroscopy, Nucleic acid tertiary structure, Nucleotide, Open-source model, Optimal matching, PatternHunter, Phylogenetic tree, Phylogenetics, Point accepted mutation, Point mutation, Probability, Protein, Protein Data Bank, Protein domain, Protein structure prediction, Reaction mechanism, Recurrence plot, Residue (chemistry), RNA, RNA editing, Root-mean-square deviation of atomic positions, Self-information, Self-similarity, Sequence assembly, Sequence homology, Sequence logo, Sequence motif, Sequential pattern mining, Side chain, Silent mutation, Simulated annealing, Single-nucleotide polymorphism, Smith–Waterman algorithm, String-searching algorithm, Structural biology, Substitution matrix, T-Coffee, Transcription factor, Translational frameshift, UGENE, X-ray crystallography, Zinc finger. Expand index (65 more) »

Accelrys

Accelrys is a software company headquartered in the United States, with representation in Europe and Asia.

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Active site

In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction.

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Additive smoothing

In statistics, additive smoothing, also called Laplace smoothing (not to be confused with Laplacian smoothing), or Lidstone smoothing, is a technique used to smooth categorical data.

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Alignment-free sequence analysis

In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches.

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Alternative splicing

Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins.

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Amino acid

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid.

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Benchmark (computing)

In computing, a benchmark is the act of running a computer program, a set of programs, or other operations, in order to assess the relative performance of an object, normally by running a number of standard tests and trials against it.

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Bioinformatics

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data.

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Biomolecular structure

Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.

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BioPerl

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

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Biopython

The Biopython Project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers.

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BioRuby

BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics.

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BLAST

In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences.

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BLOSUM

In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins.

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Bowtie (sequence analysis)

Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics.

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Burrows–Wheeler transform

The Burrows–Wheeler transform (BWT, also called block-sorting compression) rearranges a character string into runs of similar characters.

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CATH database

The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains.

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Clustal

Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence alignment.

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Coalescent theory

Coalescent theory is a model of how gene variants sampled from a population may have originated from a common ancestor.

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Comparative method

In linguistics, the comparative method is a technique for studying the development of languages by performing a feature-by-feature comparison of two or more languages with common descent from a shared ancestor, in order to extrapolate back to infer the properties of that ancestor.

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Computer memory

In computing, memory refers to the computer hardware integrated circuits that store information for immediate use in a computer; it is synonymous with the term "primary storage".

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Consensus sequence

In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment.

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Conserved sequence

In evolutionary biology, conserved sequences are similar or identical sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences) or within a genome (paralogous sequences).

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Contig

A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA.

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Convergent evolution

Convergent evolution is the independent evolution of similar features in species of different lineages.

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Data set

A data set (or dataset) is a collection of data.

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Desmond G. Higgins

Desmond Gerard Higgins is a Professor of Bioinformatics at University College Dublin, widely known for CLUSTAL, a series of computer programs for performing multiple sequence alignment.

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Distance matrix

In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set.

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DNA

Deoxyribonucleic acid (DNA) is a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.

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DNA repair

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

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DNASTAR

DNASTAR is a global bioinformatics software company incorporated in 1984 that is headquartered in Madison, Wisconsin.

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Dot plot (bioinformatics)

In bioinformatics a dot plot is a graphical method for comparing two biological sequences and identifying regions of close similarity.

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Dynamic programming

Dynamic programming is both a mathematical optimization method and a computer programming method.

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Edit distance

In computational linguistics and computer science, edit distance is a way of quantifying how dissimilar two strings (e.g., words) are to one another by counting the minimum number of operations required to transform one string into the other.

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EMBOSS

EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community.

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Enzyme

Enzymes are macromolecular biological catalysts.

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Evolution

Evolution is change in the heritable characteristics of biological populations over successive generations.

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Expressed sequence tag

In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence.

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Families of Structurally Similar Proteins database

Families of Structurally Similar Proteins or FSSP is a database of structurally superimposed proteins generated using the "Distance-matrix ALIgnment" (DALI) algorithm.

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FASTA

FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985.

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FASTA format

In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.

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FM-index

In computer science, an FM-index is a compressed full-text substring index based on the Burrows-Wheeler transform, with some similarities to the suffix array.

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Gap penalty

a Gap penalty is a method of scoring alignments of two or more sequences.

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GenBank

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations.

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Gene

In biology, a gene is a sequence of DNA or RNA that codes for a molecule that has a function.

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Genetic algorithm

In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA).

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Genetic code

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins.

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Genome

In the fields of molecular biology and genetics, a genome is the genetic material of an organism.

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Global optimization

Global optimization is a branch of applied mathematics and numerical analysis that deals with the global optimization of a function or a set of functions according to some criteria.

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Hemagglutinin

Hemagglutinin or haemagglutinin (British English)p refers to a substance that causes red blood cells (RBCs) to agglutinate.

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Heuristic

A heuristic technique (εὑρίσκω, "find" or "discover"), often called simply a heuristic, is any approach to problem solving, learning, or discovery that employs a practical method, not guaranteed to be optimal, perfect, logical, or rational, but instead sufficient for reaching an immediate goal.

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Heuristic (computer science)

In computer science, artificial intelligence, and mathematical optimization, a heuristic (from Greek εὑρίσκω "I find, discover") is a technique designed for solving a problem more quickly when classic methods are too slow, or for finding an approximate solution when classic methods fail to find any exact solution.

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Hidden Markov model

Hidden Markov Model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved (i.e. hidden) states.

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Human

Humans (taxonomically Homo sapiens) are the only extant members of the subtribe Hominina.

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Hydrophobe

In chemistry, hydrophobicity is the physical property of a molecule (known as a hydrophobe) that is seemingly repelled from a mass of water.

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Indel

Indel is a molecular biology term for an '''in'''sertion or '''del'''etion of bases in the genome of an organism.

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Inverted repeat

An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement.

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Linguistics

Linguistics is the scientific study of language, and involves an analysis of language form, language meaning, and language in context.

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List of sequence alignment software

This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment.

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Loss function

In mathematical optimization, statistics, econometrics, decision theory, machine learning and computational neuroscience, a loss function or cost function is a function that maps an event or values of one or more variables onto a real number intuitively representing some "cost" associated with the event.

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Main diagonal

In linear algebra, the main diagonal (sometimes principal diagonal, primary diagonal, leading diagonal, or major diagonal) of a matrix A is the collection of entries A_ where i.

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Margaret Oakley Dayhoff

Margaret Belle (Oakley) Dayhoff (March 11, 1925 – February 5, 1983) was an American physical chemist and a pioneer in the field of bioinformatics.

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Mathematical optimization

In mathematics, computer science and operations research, mathematical optimization or mathematical programming, alternatively spelled optimisation, is the selection of a best element (with regard to some criterion) from some set of available alternatives.

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Matrix (mathematics)

In mathematics, a matrix (plural: matrices) is a rectangular array of numbers, symbols, or expressions, arranged in rows and columns.

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Molecular clock

The molecular clock is a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged.

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Most recent common ancestor

In biology and genealogy, the most recent common ancestor (MRCA, also last common ancestor (LCA), or concestor) of any set of organisms is the most recent individual from which all the organisms are directly descended.

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Multiple sequence alignment

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.

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Natural language

In neuropsychology, linguistics, and the philosophy of language, a natural language or ordinary language is any language that has evolved naturally in humans through use and repetition without conscious planning or premeditation.

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Natural language processing

Natural language processing (NLP) is an area of computer science and artificial intelligence concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data.

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Natural selection

Natural selection is the differential survival and reproduction of individuals due to differences in phenotype.

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Needleman–Wunsch algorithm

The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences.

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NP-completeness

In computational complexity theory, an NP-complete decision problem is one belonging to both the NP and the NP-hard complexity classes.

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NP-hardness

NP-hardness (''n''on-deterministic ''p''olynomial-time hardness), in computational complexity theory, is the defining property of a class of problems that are, informally, "at least as hard as the hardest problems in NP".

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Nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei.

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Nucleic acid tertiary structure

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer.

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Nucleotide

Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth.

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Open-source model

The open-source model is a decentralized software-development model that encourages open collaboration.

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Optimal matching

Optimal matching is a sequence analysis method used in social science, to assess the dissimilarity of ordered arrays of tokens that usually represent a time-ordered sequence of socio-economic states two individuals have experienced.

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PatternHunter

PatternHunter is a commercially available homology search instrument software that uses sequence alignment techniques.

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Phylogenetic tree

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.

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Phylogenetics

In biology, phylogenetics (Greek: φυλή, φῦλον – phylé, phylon.

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Point accepted mutation

A point accepted mutation — also known as a PAM — is the replacement of a single amino acid in the primary structure of a protein with another single amino acid, which is accepted by the processes of natural selection.

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Point mutation

A point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a sequence of DNA or RNA.

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Probability

Probability is the measure of the likelihood that an event will occur.

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Protein

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.

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Protein Data Bank

The Protein Data Bank (PDB) is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.

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Protein domain

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

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Protein structure prediction

Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure.

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Reaction mechanism

In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs.

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Recurrence plot

In descriptive statistics and chaos theory, a recurrence plot (RP) is a plot showing, for a given moment in time, the times at which a phase space trajectory visits roughly the same area in the phase space.

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Residue (chemistry)

In chemistry residue is whatever remains or acts as a contaminant after a given class of events.

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RNA

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes.

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RNA editing

RNA editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase.

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Root-mean-square deviation of atomic positions

In bioinformatics, the root-mean-square deviation of atomic positions (or simply root-mean-square deviation, RMSD) is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed proteins.

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Self-information

In information theory, self-information or surprisal is the surprise when a random variable is sampled.

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Self-similarity

In mathematics, a self-similar object is exactly or approximately similar to a part of itself (i.e. the whole has the same shape as one or more of the parts).

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Sequence assembly

In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence.

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Sequence homology

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life.

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Sequence logo

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).

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Sequence motif

In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.

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Sequential pattern mining

Sequential pattern mining is a topic of data mining concerned with finding statistically relevant patterns between data examples where the values are delivered in a sequence.

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Side chain

In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called "main chain" or backbone.

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Silent mutation

Silent mutations are mutations in DNA that do not have an observable effect on the organism's phenotype.

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Simulated annealing

Simulated annealing (SA) is a probabilistic technique for approximating the global optimum of a given function.

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Single-nucleotide polymorphism

A single-nucleotide polymorphism, often abbreviated to SNP (plural), is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population (e.g. > 1%).

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Smith–Waterman algorithm

The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences.

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String-searching algorithm

In computer science, string-searching algorithms, sometimes called string-matching algorithms, are an important class of string algorithms that try to find a place where one or several strings (also called patterns) are found within a larger string or text.

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Structural biology

Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules (especially proteins, made up of amino acids, and RNA or DNA, made up of nucleic acids), how they acquire the structures they have, and how alterations in their structures affect their function.

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Substitution matrix

In bioinformatics and evolutionary biology, a substitution matrix describes the rate at which one character in a sequence changes to other character states over time.

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T-Coffee

T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach.

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Transcription factor

In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.

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Translational frameshift

Translational frameshifting or ribosomal frameshifting refers to an alternative process of protein translation.

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UGENE

UGENE is computer software for bioinformatics.

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X-ray crystallography

X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.

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Zinc finger

A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold.

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Redirects here:

Aligning sequences, Bioinformatics sequence alignment, CIGAR string, DNA Alignment, Maximal unique match, Protein sequence alignment, Sequence identity, Sequence similarity search.

References

[1] https://en.wikipedia.org/wiki/Sequence_alignment

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