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.


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

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*


  • RNA