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

Di Tommaso, Paolo; Bussotti, Giovanni, 1983-; Kemena, Carsten, 1983-; Capriotti, Emidio; Chatzou, Maria, 1985-; Prieto Barja, Pablo, 1986-; Notredame, Cedric

doi:http://dx.doi.org/10.1093/nar/gku459

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

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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

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.