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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. doi: 10.1093/nar/gku459. Epub 2014 Jun 27.

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

Author information

1
Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
3
Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48145 Münster, Germany.
4
Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 35249 Birmingham (AL), USA.
5
Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain cedric.notredame@crg.eu.

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.

PMID:
24972831
PMCID:
PMC4086076
DOI:
10.1093/nar/gku459
[Indexed for MEDLINE]
Free PMC Article

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