Consistency of optimal sequence alignments

✍ Scribed by Osamu Gotoh

• Book ID: 104271996
• Publisher: Springer
• Year: 1990
• Tongue: English
• Weight: 944 KB
• Volume: 52
• Category: Article
• ISSN: 1522-9602
• DOI: 10.1016/s0092-8240(05)80359-3

✦ Synopsis

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][360][361][362][363][364][365][366][367][368][369][370][371][372][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.