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Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. doi: 10.1093/nar/gkr335. Epub 2011 May 30.

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

Author information

1
Bioinformatics and Genomics program, Center for Genomic Regulation (CRG) and UPF, Barcelona, C/ D. Aiguader, 88, 08003 Barcelona, Spain.

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.

PMID:
21624887
PMCID:
PMC3167602
DOI:
10.1093/nar/gkr335
[Indexed for MEDLINE]
Free PMC Article

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