title: BlastR--fast and accurate database searches for non-coding RNAs.
abstract: We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.
authors.affiliation: Bioinformatics and Genomics program, Center for Genomic Regulation (CRG) and UPF, Barcelona, C/ D. Aiguader, 88, 08003 Barcelona, Spain.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussotti
authors.forename: Emanuele
authors.initials: E
authors.lastname: Raineri
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.forename: Matthias
authors.initials: M
authors.lastname: Zytnicki
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilm
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Beaudoing
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D022661:RNA, Untranslated / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D022661:RNA, Untranslated