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

Jimin Pei; Ruslan Sadreyev; Nick V. Grishin

doi:10.1093/bioinformatics/btg008

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

Jimin Pei, Ruslan Sadreyev, Nick V. Grishin

Research output: Contribution to journal › Article › peer-review

171 Scopus citations

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.

Original language	English (US)
Pages (from-to)	427-428
Number of pages	2
Journal	Bioinformatics
Volume	19
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btg008
State	Published - Feb 12 2003

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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

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