The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods

TitleThe M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods
Publication TypeJournal Article
Year of Publication2007
AuthorsMoretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C
JournalNucleic Acids Res
Volume35
PaginationW645-8
Date PublishedJul
Accession Number17526519
KeywordsAlgorithms, Amino Acid Sequence, Computational Biology/ methods, Computer Simulation, Information Storage and Retrieval, Internet, Molecular Sequence Data, Reproducibility of Results, Sequence Alignment/ methods, Sequence Homology, Amino Acid, Software, User-Computer Interface
Abstract

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.