SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
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- dc.contributor.author Di Tommaso, Paolo
- dc.contributor.author Bussotti, Giovanni, 1983-
- dc.contributor.author Kemena, Carsten, 1983-
- dc.contributor.author Capriotti, Emidio
- dc.contributor.author Chatzou, Maria, 1985-
- dc.contributor.author Prieto Barja, Pablo, 1986-
- dc.contributor.author Notredame, Cedric
- dc.date.accessioned 2024-10-21T06:30:03Z
- dc.date.available 2024-10-21T06:30:03Z
- dc.date.issued 2014
- dc.description.abstract 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.
- dc.description.sponsorship Plan Nacional [BFU2011-28575 to C.N. and P.D.]; Quantomics [KBBE-2A 222664]; Center for Genomics Regulation (CRG); La Caixa Fellowship program (to M.C.); Spanish Ministry of Economy and Competitiveness [BES-2012–051918 to P.B.]. EMBL Interdisciplinary Postdoc (EIPOD) under Marie Curie Actions (COFUND) (to G.B.); Department of Pathology at the University of Alabama at Birmingham (to E.C.). Funding for open access charge: Plan Nacional [BFU2011-28575 to C.N. and P.D.]; Quantomics [KBBE-2A 222664]; Center for Genomics Regulation (CRG); La Caixa Fellowship program (to M.C.); Spanish Ministry of Economy and Competitiveness [BES-2012–051918 to P.B.]. EMBL Interdisciplinary Postdoc (EIPOD) under Marie Curie Actions (COFUND) (to G.B.); Department of Pathology at the University of Alabama at Birmingham (to E.C.); Computational resources are provided by the Center for Genomic Regulation (CRG).
- dc.format.mimetype application/pdf
- dc.identifier.citation Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, et al. SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. Nucleic Acids Res. 2014 Jul 1;42(W1):W356-60. DOI: 10.1093/nar/gku459
- dc.identifier.doi http://dx.doi.org/10.1093/nar/gku459
- dc.identifier.issn 0305-1048
- dc.identifier.uri http://hdl.handle.net/10230/68258
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Nucleic Acids Research. 2014 Jul 1;42(W1):W356-60
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/222664
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011-28575
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BES2012–051918
- dc.rights © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. 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
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
- dc.subject.other Filogènia
- dc.subject.other Ribonucleases
- dc.subject.other Proteïnes
- dc.title SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion