BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res 39: 6886

We present and validate BlastR, a method for effi-ciently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleo-tides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like se-quences. 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 effect-ive when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html