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Bioinformatics. 2003 Feb 12;19(3):427-8.

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

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


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.


PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from

[Indexed for MEDLINE]

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