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

Jimin Pei, Ruslan Sadreyev, Nick V. Grishin

Research output: Contribution to journalArticle

168 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 languageEnglish (US)
Pages (from-to)427-428
Number of pages2
JournalBioinformatics
Volume19
Issue number3
DOIs
StatePublished - Feb 12 2003

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ASJC Scopus subject areas

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

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