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- Title
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
- Authors
Pei, Jimin; Sadreyev, Ruslan; Grishin, Nick V
- Abstract
PCMA (profile consistency multiple sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies. Highly similar sequences are aligned in a fast way as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is applied to align the relatively divergent groups based on profile-profile comparison and consistency. The scoring function for local alignments of pre-aligned groups is based on a novel profile-profile comparison method that is a generalization of the PSI-BLAST approach to profile-sequence comparison. PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences.
- Publication
Bioinformatics (Oxford, England), 2003, Vol 19, Issue 3, p427
- ISSN
1367-4803
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btg008