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Title:
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T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
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Author:
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Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg Cortada, Miquel; Montañola Lacort, Alberto
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Notes:
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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.
Funding for open access charge: Plan Nacional (BFU2008-00419 to C.N. and P.D.T.); 7th Framework Programme of the European Commission, the LEISHDRUG (no 223414) and the Quantomics (KBBE-2A-222664) project; Computational resources are provided by the Center for Genomic Regulation (CRG) of Barcelona and the Vital-IT ( http://www.vital-it.ch ) Center for high-performance computing of the Swiss Institute of Bioinformatics; CUR of DIUE of GENCAT (to M.O. and A.M.); the Spanish ministry of education (TIN2008-05913); Consolider project (CSD 2007-00050);’ Super-computacion y e-Ciencia (SYEC)’. |
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Subject(s):
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-T-Coffee
-Algorismes computacionals
-Processament electrònic de dades -- Disseny de sistemes |
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Rights:
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cc-by-nc, (c) Di Tommaso et al., 2011
http://creativecommons.org/licenses/by-nc/3.0/es/deed.ca
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Document type:
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article
publishedVersion |
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Published by:
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Oxford University Press
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Share:
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