101. BlastR—fast and accurate database searches for non-coding RNAs
- Author
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Bussotti, Giovanni, Raineri, Emanuele, Erb, Ionas, Zytnicki, Matthias, Wilm, Andreas, Beaudoing, Emmanuel, Bucher, Philipp, Notredame, Cedric, Bussotti, Giovanni, Raineri, Emanuele, Erb, Ionas, Zytnicki, Matthias, Wilm, Andreas, Beaudoing, Emmanuel, Bucher, Philipp, and Notredame, Cedric
- 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
- Published
- 2017