Skip Navigation



Nucleic Acids Research Advance Access published online on April 17, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn174
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1373K) Freely available
Right arrow Screen PDF (296K) Freely available
Right arrowOA All Versions of this Article:
36/9/e52    most recent
gkn174v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Wilm, A.
Right arrow Articles by Notredame, C.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wilm, A.
Right arrow Articles by Notredame, C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

R-Coffee: a method for multiple alignment of non-coding RNA

Andreas Wilm1, Desmond G. Higgins1 and Cédric Notredame2,*

1The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 2Centre for Genomic Regulation (CRG), Dr Aiguader, 88, 08003 Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 93 316 02 71; Fax: +34 93 316 00 99; Email: cedric.notredame{at}crg.es

Received December 20, 2007. Revised March 14, 2008. Accepted March 25, 2008.

R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align RNA sequences while exploiting secondary structure information. R-Coffee uses an alignment-scoring scheme that incorporates secondary structure information within the alignment. It works particularly well as an alignment improver and can be combined with any existing sequence alignment method. In this work, we used R-Coffee to compute multiple sequence alignments combining the pairwise output of sequence aligners and structural aligners. We show that R-Coffee can improve the accuracy of all the sequence aligners. We also show that the consistency-based component of T-Coffee can improve the accuracy of several structural aligners. R-Coffee was tested on 388 BRAliBase reference datasets and on 11 longer Cmfinder datasets. Altogether our results suggest that the best protocol for aligning short sequences (less than 200 nt) is the combination of R-Coffee with the RNA pairwise structural aligner Consan. We also show that the simultaneous combination of the four best sequence alignment programs with R-Coffee produces alignments almost as accurate as those obtained with R-Coffee/Consan. Finally, we show that R-Coffee can also be used to align longer datasets beyond the usual scope of structural aligners. R-Coffee is freely available for download, along with documentation, from the T-Coffee web site (www.tcoffee.org).


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.