PCMA: fast and accurate multiple sequence alignment based on profile consistency. 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/.
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References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
- Mora-Gutiérrez, Roman Anselmo; Lárraga-Ramírez, María E.; Rincón-García, Eric A.; Ponsich, Antonin; Ramírez-Rodríguez, Javier: Adaptation of the method of musical composition for solving the multiple sequence alignment problem (2015)
- Petitjean, François; Gançarski, Pierre: Summarizing a set of time series by averaging: from Steiner sequence to compact multiple alignment (2012)
- Petitjean, François; Ketterlin, Alain; Gançarski, Pierre: A global averaging method for dynamic time warping, with applications to clustering (2011)