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

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


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/.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Algorithms*
  • Database Management Systems*
  • Quality Control
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software*