Nucleic Acids Research Advance Access originally published online on May 15, 2008
Nucleic Acids Research 2008 36(Web Server issue):W10-W13; doi:10.1093/nar/gkn278
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W10-W13
© 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.
Articles |
R-Coffee: a web server for accurately aligning noncoding RNA sequences
1Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3Centre for Genomic Regulation (CRG), UPF, 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 January 30, 2008. Revised April 16, 2008. Accepted April 26, 2008.
The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple sequence alignment (MSA) methods to compute a primary library of input alignments. The program then computes an MSA highly consistent with both the alignments contained in the library and the secondary structures associated with the sequences. The secondary structures are predicted using RNAplfold. The server provides two modes. The slow/accurate mode is restricted to small datasets (less than 5 sequences less than 150 nucleotides) and combines R-Coffee with Consan, a very accurate pairwise RNA alignment method. For larger datasets a fast method can be used (RM-Coffee mode), that uses R-Coffee to combine the output of the three packages which combines the outputs from programs found to perform best on RNA (MUSCLE, MAFFT and ProbConsRNA). Our BRAliBase benchmarks indicate that the R-Coffee/Consan combination is one of the best ncRNA alignment methods for short sequences, while the RM-Coffee gives comparable results on longer sequences. The R-Coffee web server is available at http://www.tcoffee.org.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors