About: Multiple sequence alignment

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Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more

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rdf:type	architectural structure
rdfs:label	Multiple sequence alignment (en)
rdfs:comment	Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more (en)
sameAs	Multiple sequence alignment Multiple sequence alignment
dbp:wikiPageUsesTemplate	dbt:Cite_book dbt:Cite_journal dbt:Good_article dbt:Reflist dbt:Short_description
Subject	Bioinformatics Computational phylogenetics Markov models
gold:hypernym	Alignment
prov:wasDerivedFrom	http://en.wikipedia.org/wiki/Multiple_sequence_alignment?oldid=1048784914&ns=0
Wikipage page ID	4066308 (xsd:integer)
page length (characters) of wiki page	52391 (xsd:nonNegativeInteger)
Wikipage revision ID	1048784914 (xsd:integer)
Link from a Wikipage to another Wikipage	NP-completeness Nucleotide Protein Protein domain Protein structure prediction T-Coffee Additive smoothing Algorithm Alignment-free sequence analysis Amino acid Benders decomposition Big O notation Biomolecular structure Sequence alignment Sequence motif Viterbi algorithm Branch and price CASP Bioinformatics Computational phylogenetics Generalized tree alignment Genetic algorithm Gibbs sampling Global optimization Jalview Markov models Directed acyclic graph Hill climbing Mutation PANDIT (database) Phylogenetical Phylogenetical Quantum computing Cladistics D-Wave Systems D-na Linear programming List of sequence alignment software Time complexity Clustal Cluster analysis Algorithmic complexity Conserved sequence Dynamic programming Heuristic Hidden Markov model Homology (biology) List of alignment visualization software Ribosomal frameshift Saccharomyces cerevisiae Gap penalty Graph Indel Evolution Exon Expectation–maximization algorithm FASTA HH-suite HMMER Molecular phylogenetics UGENE UPGMA European Molecular Biology Laboratory Structural alignment Substitution matrix Loss function MAFFT MUSCLE (alignment software) Mathematical optimization Multiple EM for Motif Elicitation Neighbor joining RNA RNA splicing Simulated annealing Yeast
has abstract	Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. Computational algorithms are used to produce and analyse the MSAs due to the difficulty and intractability of manually processing the sequences given their biologically-relevant length. MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. On the other hand, heuristic methods generally fail to give guarantees on the solution quality, with heuristic solutions shown to be often far below the optimal solution on benchmark instances. (en)
foaf:isPrimaryTopicOf	http://en.wikipedia.org/wiki/Multiple_sequence_alignment
is rdfs:seeAlso of	Phylo (video game)

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