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Comparative Study
. 2003 Feb 12;19(3):427-8.
doi: 10.1093/bioinformatics/btg008.

PCMA: fast and accurate multiple sequence alignment based on profile consistency

Jimin Pei  1 , Ruslan Sadreyev, Nick V Grishin
Affiliations
Comparative Study

PCMA: fast and accurate multiple sequence alignment based on profile consistency

Jimin Pei et al. Bioinformatics. .

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.

Availability: PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/.

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