title: SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.
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.
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors: Paolo
authors: P
authors: Di Tommaso
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors: Giovanni
authors: G
authors: Bussotti
authors: Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48145 Münster, Germany.
authors: Carsten
authors: C
authors: Kemena
authors: Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 35249 Birmingham (AL), USA.
authors: Emidio
authors: E
authors: Capriotti
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors: Maria
authors: M
authors: Chatzou
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors: Pablo
authors: P
authors: Prieto
authors: 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.
authors: Cedric
authors: C
authors: Notredame
mesh_terms: D000465:Algorithms; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA