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

被引：797

作者：

Di Tommaso, Paolo ^{[1
]}

Moretti, Sebastien ^{[2
,3
]}

Xenarios, Ioannis ^{[2
]}

Orobitg, Miquel ^{[4
]}

Montanyola, Alberto ^{[4
]}

Chang, Jia-Ming ^{[1
]}

Taly, Jean-Francois ^{[1
]}

Notredame, Cedric ^{[1
]}

机构：

[1] Pompeu Fabra Univ, Ctr Genom Regulat, Barcelona 08003, Spain

[2] Swiss Inst Bioinformat, Vital IT, CH-1015 Lausanne, Switzerland

[3] Univ Lausanne, Dept Ecol & Evolut Biophore, CH-1015 Lausanne, Switzerland

[4] Univ Lleida, Dept Comp Sci & Ind Engn, E-25001 Lleida, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

ACCURACY;

D O I：

10.1093/nar/gkr245

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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://tcoffee.crg.cat.

引用

页码：W13 / W17

页数：5

共 25 条

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