BlastR-fast and accurate database searches for non-coding RNAs

Giovanni Bussotti (1) , Emanuele Raineri (1, 2) , Ionas Erb (1) , Matthias Zytnicki (3, 1) , Andreas Wilm (4) , Emmanuel Beaudoing (1, 5) , Philipp Bucher (6, 7) , Cedric Notredame (1)

1 Bioinformatics and Genomics Program
2 Centro Nacional de Análisis Genómico
3 URGI - Unité de Recherche Génomique Info
4 UCD - University College Dublin
5 UNIL - Université de Lausanne = University of Lausanne
6 Swiss Institute for Experimental Cancer Research
7 SIB - Swiss Institute of Bioinformatics [Lausanne]

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.

Mots clés: RNAs; algorithms; sequence alignment; software

Domaines: Sciences du Vivant [q-bio]; Biologie végétale

Giovanni Bussotti, Emanuele Raineri, Ionas Erb, Matthias Zytnicki, Andreas Wilm, et al.. BlastR-fast and accurate database searches for non-coding RNAs. Nucleic Acids Research, 2011, 39 (16), pp.6886-6895. ⟨10.1093/nar/gkr335⟩. ⟨hal-02644812⟩