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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
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-...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125728/ https://www.ncbi.nlm.nih.gov/pubmed/21558174 http://dx.doi.org/10.1093/nar/gkr245 |
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author | Di Tommaso, Paolo Moretti, Sebastien Xenarios, Ioannis Orobitg, Miquel Montanyola, Alberto Chang, Jia-Ming Taly, Jean-François Notredame, Cedric |
author_facet | Di Tommaso, Paolo Moretti, Sebastien Xenarios, Ioannis Orobitg, Miquel Montanyola, Alberto Chang, Jia-Ming Taly, Jean-François Notredame, Cedric |
author_sort | Di Tommaso, Paolo |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-3125728 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257282011-07-05 T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension Di Tommaso, Paolo Moretti, Sebastien Xenarios, Ioannis Orobitg, Miquel Montanyola, Alberto Chang, Jia-Ming Taly, Jean-François Notredame, Cedric Nucleic Acids Res Articles 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. Oxford University Press 2011-07-01 2011-05-09 /pmc/articles/PMC3125728/ /pubmed/21558174 http://dx.doi.org/10.1093/nar/gkr245 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Di Tommaso, Paolo Moretti, Sebastien Xenarios, Ioannis Orobitg, Miquel Montanyola, Alberto Chang, Jia-Ming Taly, Jean-François Notredame, Cedric T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title | T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title_full | T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title_fullStr | T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title_full_unstemmed | T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title_short | T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension |
title_sort | t-coffee: a web server for the multiple sequence alignment of protein and rna sequences using structural information and homology extension |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125728/ https://www.ncbi.nlm.nih.gov/pubmed/21558174 http://dx.doi.org/10.1093/nar/gkr245 |
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