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Consistency of optimal sequence alignments.

O Gotoh
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Abstract

Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a "skeletal representation" (Bull. math. Biol. 52, 359-373). This method is further extended so that the combination of pairwise alignments that gives the greatest consistency is found when possibly many alignments are equally optimal for each pairwise comparison. A method for acceleration of simultaneous multiple sequence alignment is proposed in which consistent regions serve as "anchor points" limiting application of direct multi-way alignment to the rest of "inconsistent" regions.

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AlgorithmsBase SequenceMolecular Sequence DataRNASequence Homology, Nucleic AcidJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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O Gotoh. 1990. Consistency of optimal sequence alignments.. https://doi.org/10.1007/bf02462264

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PubMed2026

Theseus: fast and optimal affine-gap sequence-to-graph alignment.

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