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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. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are…

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Overview

Interpretation

Alignment methods

Representations

Global and local alignments

Pairwise alignment

Dynamic programming

Multiple sequence alignment

Structural alignment

Phylogenetic analysis

Other biological uses

Non-biological uses

Software

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Map overview Semantic statistics

Sequence alignment

Nodes130
Edges129
Triples152
Avg. degree1.98
Density0.015385
Components1

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Sequence alignment

Top relations

related to Representations · 22
Sequence alignment → Alignments, As, BioPerl, BioPython, BioRuby, CIGAR, Compact Idiosyncratic Gapped Alignment, DNA, EMBOSS, FASTA, For, GenBank, In, Many, Most, READSEQ, Report, RNA, Sequence, Several
has method · 16
Sequence alignment → By, Calculating, Clustal, Computational, FASTA, However, Iterative, Local, Many, Most, Progressive, T-Coffee, The, These, Various, Very
related to Maximal unique match · 13
Sequence alignment → Anchors, Finally, Identification, Longer MUM, Match, More, MUM, MUMmer, MUMs, One, The, To, Unique
related to Software · 13
Sequence alignment → Alignment, BAliBASE, BLAST, ClustalW2, Commercial, DNASTAR Lasergene, FASTA3x, Geneious, PatternHunter, STRAP, T-coffee, The, Tools
related to Phylogenetic analysis · 12
Sequence alignment → Commonly, DNA, In, More, NP-hard, Other, Phylogenetics, Progressive, Roughly, The, Therefore, This
related to Techniques inspired by computer science · 9
Sequence alignment → Bowtie, BWA, Genetic, Hidden Markov, HMM-based, More, See FM-index, The Burrows, Wheeler
related to Assessment of significance · 7
Sequence alignment → Alignments, BLAST, However, In, Repetitive, Sequence, These
related to Dynamic programming · 6
Sequence alignment → Although, MSA, One, Standard, The, This
related to Non-biological uses · 6
Sequence alignment → Business, In, Needleman-Wunsch, Optimal, Techniques, The
related to Interpretation · 5
Sequence alignment → Although DNA, If, In, RNA, The

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Important terminology

sequence alignment sequences alignments methods used multiple query also protein two structural method aligned database similar pairwise dynamic programming matrix

Entity relationships Subject–Predicate–Object triples

SubjectPredicateObjectConfidenceSrc
Sequence alignmentis away of arranging the sequences of DNA0.90text
Sequence alignmentis aextension of pairwise alignment to incorporate more than two sequences at a time0.90text
calculating the distance cost between strings in a natural languageinstance ofSequence alignments are also used for non-biological sequences0.80text
or to display financial datainstance ofSequence alignments are also used for non-biological sequences0.80text
MUMmerinstance ofis the first step in larger alignment systems0.80text
GeneWiseinstance ofMore general methods are available from open-source software0.80text
Bowtieinstance ofWheeler transform has been successfully applied to fast short read alignment in popular tools0.80text
BWAinstance ofWheeler transform has been successfully applied to fast short read alignment in popular tools0.80text
rigid-body root mean square distanceinstance ofBased on measures0.80text
residue distancesinstance ofBased on measures0.80text
local secondary structureinstance ofBased on measures0.80text
and surrounding environmental features such as residue neighbor hydrophobicityinstance ofBased on measures0.80text

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