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Oxford University Press, Nucleic Acids Research, suppl(39), p. W13-W17, 2011

DOI: 10.1093/nar/gkr245

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

Journal article published in 2011 by Paolo Di Tommaso, 張家銘, Sebastien Moretti, Ioannis Xenarios ORCID, Miquel Orobitg, Di;Paolo;Moretti Sebastien;Xenarios Ioannis;Orobitg Miquel;Montanyola Alberto;Chang Jia-Ming;Taly Jean-François;Notredame Cedric Tommaso, Alberto Montanyola, J.-M. Chang ORCID, J.-F. Taly, Cedric Notredame
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.