T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

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2011
Author
Di Tommaso, Paolo
Moretti, Sebastien
Xenarios, Ioannis
Orobitg Cortada, Miquel
Montañola Lacort, Alberto
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Abstract
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee
mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
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http://hdl.handle.net/10459.1/46369
DOI
https://doi.org/10.1093/nar/gkr245
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Nucleic Acids Research, 2011, vol. 39, supl. 2 (Web Server issue), W13-17
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cc-by-nc, (c) Di Tommaso et al., 2011
Except where otherwise noted, this item's license is described as cc-by-nc, (c) Di Tommaso et al., 2011