Abstract:
:We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from http://www.tcoffee.org/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wallace IM,O'Sullivan O,Higgins DG,Notredame Cdoi
10.1093/nar/gkl091keywords:
subject
Has Abstractpub_date
2006-03-23 00:00:00pages
1692-9issue
6eissn
0305-1048issn
1362-4962pii
34/6/1692journal_volume
34pub_type
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