SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequen...

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Detalles Bibliográficos
Autores principales: Di Tommaso, Paolo, Bussotti, Giovanni, Kemena, Carsten, Capriotti, Emidio, Chatzou, Maria, Prieto, Pablo, Notredame, Cedric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086076/
https://www.ncbi.nlm.nih.gov/pubmed/24972831
http://dx.doi.org/10.1093/nar/gku459
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author Di Tommaso, Paolo
Bussotti, Giovanni
Kemena, Carsten
Capriotti, Emidio
Chatzou, Maria
Prieto, Pablo
Notredame, Cedric
author_facet Di Tommaso, Paolo
Bussotti, Giovanni
Kemena, Carsten
Capriotti, Emidio
Chatzou, Maria
Prieto, Pablo
Notredame, Cedric
author_sort Di Tommaso, Paolo
collection PubMed
description This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee.
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spelling pubmed-40860762014-10-28 SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments Di Tommaso, Paolo Bussotti, Giovanni Kemena, Carsten Capriotti, Emidio Chatzou, Maria Prieto, Pablo Notredame, Cedric Nucleic Acids Res Article This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. Oxford University Press 2014-07-01 2014-06-27 /pmc/articles/PMC4086076/ /pubmed/24972831 http://dx.doi.org/10.1093/nar/gku459 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Article
Di Tommaso, Paolo
Bussotti, Giovanni
Kemena, Carsten
Capriotti, Emidio
Chatzou, Maria
Prieto, Pablo
Notredame, Cedric
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title_full SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title_fullStr SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title_full_unstemmed SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title_short SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
title_sort sara-coffee web server, a tool for the computation of rna sequence and structure multiple alignments
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086076/
https://www.ncbi.nlm.nih.gov/pubmed/24972831
http://dx.doi.org/10.1093/nar/gku459
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