title: 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.
authors.affiliation: Centre For Genomic Regulation (Pompeu Fabra University), Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Paolo
authors.initials: P
authors.lastname: Di Tommaso
authors.forename: Sebastien
authors.initials: S
authors.lastname: Moretti
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Miquel
authors.initials: M
authors.lastname: Orobitg
authors.forename: Alberto
authors.initials: A
authors.lastname: Montanyola
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Taly
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA