Published online 23 March 2006
Computational Method and +G1 Genomics |
M-Coffee: combining multiple sequence alignment methods with T-Coffee
The Conway Institute of Biomolecular and Biomedical Research, University College Dublin Ireland 1Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) Parc Scientifique de Luminy, 163 Avenue de Luminy, 13288, Marseille cedex 09, France
*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame{at}europe.com
Received January 19, 2006. Revised February 7, 2006. Accepted March 7, 2006.
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/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. M Dahms, L. J Olson, and J.-J. P Kim Strategies for carbohydrate recognition by the mannose 6-phosphate receptors Glycobiology, September 1, 2008; 18(9): 664 - 678. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Rausch, A.-K. Emde, D. Weese, A. Doring, C. Notredame, and K. Reinert Segment-based multiple sequence alignment Bioinformatics, August 15, 2008; 24(16): i187 - i192. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Katoh and H. Toh Recent developments in the MAFFT multiple sequence alignment program Brief Bioinform, July 1, 2008; 9(4): 286 - 298. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. B. Do, C.-S. Foo, and S. Batzoglou A max-margin model for efficient simultaneous alignment and folding of RNA sequences Bioinformatics, July 1, 2008; 24(13): i68 - i76. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Moretti, A. Wilm, D. G. Higgins, I. Xenarios, and C. Notredame R-Coffee: a web server for accurately aligning noncoding RNA sequences Nucleic Acids Res., July 1, 2008; 36(suppl_2): W10 - W13. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Liu, S. Louie, W. Hsu, K. M. Yu, H. B. Nicholas Jr., and G. L. Rosenquist Tyrosine Sulfation Is Prevalent in Human Chemokine Receptors Important in Lung Disease Am. J. Respir. Cell Mol. Biol., June 1, 2008; 38(6): 738 - 743. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Wilm, D. G. Higgins, and C. Notredame R-Coffee: a method for multiple alignment of non-coding RNA Nucleic Acids Res., May 1, 2008; 36(9): e52 - e52. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. P. Fournier and J. P. Gogarten Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol., February 1, 2008; 190(3): 1124 - 1127. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Occhino, F. Ghiotto, S. Soro, M. Mortarino, S. Bosi, M. Maffei, S. Bruno, M. Nardini, M. Figini, A. Tramontano, et al. Dissecting the Structural Determinants of the Interaction between the Human Cytomegalovirus UL18 Protein and the CD85j Immune Receptor J. Immunol., January 15, 2008; 180(2): 957 - 968. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Moretti, F. Armougom, I. M. Wallace, D. G. Higgins, C. V. Jongeneel, and C. Notredame The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods Nucleic Acids Res., July 13, 2007; 35(suppl_2): W645 - W648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Pagni, V. Ioannidis, L. Cerutti, M. Zahn-Zabal, C. V. Jongeneel, J. Hau, O. Martin, D. Kuznetsov, and L. Falquet MyHits: improvements to an interactive resource for analyzing protein sequences Nucleic Acids Res., July 13, 2007; 35(suppl_2): W433 - W437. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. T. Ranjith-Kumar, W. Miller, J. Sun, J. Xiong, J. Santos, I. Yarbrough, R. J. Lamb, J. Mills, K. E. Duffy, S. Hoose, et al. Effects of Single Nucleotide Polymorphisms on Toll-like Receptor 3 Activity and Expression in Cultured Cells J. Biol. Chem., June 15, 2007; 282(24): 17696 - 17705. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Capul, T. Barron, D. E. Dobson, S. J. Turco, and S. M. Beverley Two Functionally Divergent UDP-Gal Nucleotide Sugar Transporters Participate in Phosphoglycan Synthesis in Leishmania major J. Biol. Chem., May 11, 2007; 282(19): 14006 - 14017. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kumar and A. Filipski Multiple sequence alignment: In pursuit of homologous DNA positions Genome Res., February 1, 2007; 17(2): 127 - 135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Yang, G. A. Tuskan, and Z.-M. Cheng Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication Plant Physiology, November 1, 2006; 142(3): 820 - 830. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Pei and N. V. Grishin MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information Nucleic Acids Res., September 11, 2006; 34(16): 4364 - 4374. [Abstract] [Full Text] [PDF]
|
|