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2011
- doi: 10.1093/nar/gkr335
- issn: 0305-1048
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Software, Free computer Free software Freeware Public domain software Ribose nucleic acid Ribonucleic acid Exchange standard, Gold Gold exchange standard Standard, Gold Noncoding RNA ncRNA Small RNA Non-translated RNA Functional RNA nmRNA Small non-messenger RNA snmRNA sRNA Nontranslated RNA Non-messenger RNA Untranslated RNA fRNACiter ce document
G. Bussotti et al., « BlastR--fast and accurate database searches for non-coding RNAs. », Serveur académique Lausannois, ID : 10.1093/nar/gkr335
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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.