Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. Epub 2011 May 9.

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

Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.

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Centre For Genomic Regulation (Pompeu Fabra University), Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.

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.

PMID:: 21558174; [PubMed - indexed for MEDLINE]
PMCID:: PMC3125728

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Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. [Nat Protoc. 2011]
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