dc.contributor.author |
Di Tommaso, Paolo |
dc.contributor.author |
Moretti, Sebastien |
dc.contributor.author |
Xenarios, Ioannis |
dc.contributor.author |
Orobitg Cortada, Miquel |
dc.contributor.author |
Montañola Lacort, Alberto |
dc.date |
2012-12-11T10:05:27Z |
dc.date |
2012-12-11T10:05:27Z |
dc.date |
2011 |
dc.identifier |
0305-1048 |
dc.identifier |
http://hdl.handle.net/10459.1/46369 |
dc.identifier |
https://doi.org/10.1093/nar/gkr245 |
dc.identifier.uri |
http://hdl.handle.net/10459.1/46369 |
dc.description |
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. |
dc.description |
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)’. |
dc.language |
eng |
dc.publisher |
Oxford University Press |
dc.relation |
MICINN/PN2008-2011/BFU2008-00419 |
dc.relation |
MICINN/PN2008-2011/TIN2008-05913 |
dc.relation |
MIECI/PN2004-2007/CSD 2007-00050 |
dc.relation |
Reproducció del document publicat a: https://doi.org/10.1093/nar/gkr245 |
dc.relation |
Nucleic Acids Research, 2011, vol. 39, supl. 2 (Web Server issue), W13-17 |
dc.relation |
info:eu-repo/grantAgreement/EC/FP7/223414 |
dc.relation |
info:eu-repo/grantAgreement/EC/FP7/KBBE-2A-222664 |
dc.rights |
cc-by-nc, (c) Di Tommaso et al., 2011 |
dc.rights |
http://creativecommons.org/licenses/by-nc/3.0/es/deed.ca |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.subject |
T-Coffee |
dc.subject |
Algorismes computacionals |
dc.subject |
Processament electrònic de dades -- Disseny de sistemes |
dc.title |
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
dc.type |
article |
dc.type |
publishedVersion |