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

Paolo Di Tommaso; Giovanni Bussotti; Carsten Kemena; Emidio Capriotti; Maria Chatzou; Pablo Prieto; Cedric Notredame

doi:10.1093/nar/gku459

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

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

Authors

Paolo Di Tommaso¹, Giovanni Bussotti², Carsten Kemena³, Emidio Capriotti⁴, Maria Chatzou¹, Pablo Prieto¹, Cedric Notredame⁵

Affiliations

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Internet
Nucleic Acid Conformation
RNA / chemistry*
Sequence Alignment / methods*
Sequence Analysis, RNA / methods*
Software*

Substances

RNA