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

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.

Figure 1.

Sample T-Coffee result page. The top part is a color-coded alignment where sequences in red correspond to alignment portions with a strong support in the primary library. For post-processing purpose, users are advised to download the text-based version of the alignment available in the Result files section.