M-Coffee: combining multiple sequence alignment methods with T-Coffee

By Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins, Cédric Notredame. Nucleic Acids Research, 2006

612 citations recorded by the source corpus.

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 .

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c7b2369c4c010ed91eddbce27d80903575610532

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Citations in the corpus

Phylogeny of the gastropod superfamily Cerithioidea using morphology and molecules (2011, methodology): “Attempts were made to obtain a better alignment using MUSCLE (Edgar, 2004) (default settings and –refine option), T-Coffee (Notredame, Higgins & Heringa, 2000), or the M-Coffee method of combining and refining alignments produced by a variety of other programs (Wallace et al., 2006).”
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning (2013, methodology): “Then we integrate the predicted probability as a prior into our GGL to further improve the accuracy of joint EC analysis.”
RAD51 and Breast Cancer Susceptibility: No Evidence for Rare Variant Association in the Breast Cancer Family Registry Study (2012, positive): “cat/apps/tcoffee/ do:mcoffee), which is part of the T-Coffee (Tree-based Consistency Objective Function for alignment Evaluation) software suite of alignment tools [53,54], to prepare a RAD51 protein multiple sequence alignment with 15 RAD51 orthologs, in which the most diverged sequence was from fr”
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension (2011, methodology): “One can even use pre-existing multiple sequence alignment methods, like in the M-Coffee protocol (14) where the library is made of a collection of multiple sequence alignment produced with third-party multiple aligners.”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “M-Coffee (64) was used to generate a consensus version of the four alignments.”
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (2010, background): “The six resulting alignments are then combined with M-Coffee (23).”
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences (2007, background): “A few other strategies combine alignments from existing algorithms to obtain an improved alignment (Bucka-Lassen et al. 1999; Wallace et al. 2006).”
Ensembl’s 10th year (2009, methodology): “The latest improvements include the use of the meta-aligner M-Coffee (23) and incorporation of information about exon boundaries into the alignments.”