R-Coffee: a web server for accurately aligning noncoding RNA sequences.
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.
Moretti
Sébastien
S
Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland.
Wilm
Andreas
A
Higgins
Desmond G
DG
Xenarios
Ioannis
I
Notredame
Cédric
C
D000465:Algorithms; D020407:Internet; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA; D012984:Software
D022661:RNA, Untranslated