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© Research
Publication : Nucleic acids research

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Nucleic acids research - 30 May 2011

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C

Link to Pubmed [PMID] – 21624887

Nucleic Acids Res. 2011 Sep;39(16):6886-95

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.

https://www.ncbi.nlm.nih.gov/pubmed/21624887