title: PCMA: fast and accurate multiple sequence alignment based on profile consistency.
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.
  
  
  BACKGROUND
  PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/.
authors.affiliation: Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA. jpei@mednet.swmed.edu
authors.forename: Jimin
authors.initials: J
authors.lastname: Pei
authors.forename: Ruslan
authors.initials: R
authors.lastname: Sadreyev
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D011786:Quality Control; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software