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Bioinformatics Vol. 19 no. 3 2003
Pages 427-428
© 2003 Oxford University Press

Applications Note

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

Jimin Pei , Ruslan Sadreyev and Nick V. Grishin *

Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA

Received on August 14, 2002 ; revised on October 21, 2002 ; accepted on October 21, 2002

Summary: 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/

Contact: jpei{at}mednet.swmed.edu grishin{at}chop.swmed.edu

* To whom correspondence should be addressed.


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