BlastR-fast and accurate database searches for non-coding RNAs
Bussotti, Giovanni | Raineri, Emanuele | Erb, Ionas | Zytnicki, Matthias | Wilm, Andreas | Beaudoing, Emmanuel | Bucher, Philipp | Notredame, Cedric | Bioinformatics and Genomics Program ; Centre for Genomic Regulation (CRG) | Centro Nacional de Análisis Genómico | Unité de Recherche Génomique Info (URGI) ; Institut National de la Recherche Agronomique (INRA) | University College Dublin [Dublin] (UCD) | Université de Lausanne = University of Lausanne (UNIL) | Swiss Institute for Experimental Cancer Research | Swiss Institute of Bioinformatics [Lausanne] (SIB) ; Université de Lausanne = University of Lausanne (UNIL)
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Показать больше [+] Меньше [-]Английский. 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.
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