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

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Serval ID
serval:BIB_2CC4F1845EB4
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
BlastR--fast and accurate database searches for non-coding RNAs.
Journal
Nucleic Acids Research
Author(s)
Bussotti G., Raineri E., Erb I., Zytnicki M., Wilm A., Beaudoing E., Bucher P., Notredame C.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2011
Volume
39
Number
16
Pages
6886-6895
Language
english
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.
Pubmed
Web of science
Open Access
Yes
Create date
06/06/2011 7:29
Last modification date
20/08/2019 13:11
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