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

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Abstract
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@mednet.swmed.edu grishin@chop.swmed.edu

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