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

TitleT-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Publication TypeJournal Article
Year of Publication2011
AuthorsDi Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C
JournalNucleic acids research
Date PublishedMay
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.

URLhttp://dx.doi.org/10.1093/nar/gkr245
DOI10.1093/nar/gkr245