000170995 001__ 170995
000170995 005__ 20190316235238.0
000170995 0247_ $$2doi$$a10.1093/nar/gkr335
000170995 022__ $$a0305-1048
000170995 02470 $$2ISI$$a000294556800011
000170995 037__ $$aARTICLE
000170995 245__ $$aBlastR-fast and accurate database searches for non-coding RNAs
000170995 269__ $$a2011
000170995 260__ $$bOxford University Press$$c2011
000170995 336__ $$aJournal Articles
000170995 520__ $$aWe 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.
000170995 6531_ $$aSecondary Structure
000170995 6531_ $$aSequence Alignment
000170995 6531_ $$aCovariance-Models
000170995 6531_ $$aNucleotide
000170995 6531_ $$aAlgorithm
000170995 6531_ $$aElements
000170995 6531_ $$aIdentification
000170995 6531_ $$aSubstitution
000170995 6531_ $$aEvolution
000170995 6531_ $$aFrequency
000170995 700__ $$aBussotti, Giovanni
000170995 700__ $$aRaineri, Emanuele
000170995 700__ $$aErb, Ionas
000170995 700__ $$aZytnicki, Matthias
000170995 700__ $$aWilm, Andreas
000170995 700__ $$aBeaudoing, Emmanuel
000170995 700__ $$0244404$$aBucher, Philipp$$g113607
000170995 700__ $$aNotredame, Cedric
000170995 773__ $$j39$$k16$$q6886-6895$$tNucleic Acids Research
000170995 8564_ $$s3187341$$uhttps://infoscience.epfl.ch/record/170995/files/6886.full.pdf$$yPublisher's version$$zPublisher's version
000170995 909C0 $$0252244$$pGR-BUCHER$$xU11780
000170995 909CO $$ooai:infoscience.tind.io:170995$$pSV$$particle$$qGLOBAL_SET
000170995 917Z8 $$x182396
000170995 937__ $$aEPFL-ARTICLE-170995
000170995 973__ $$aEPFL$$rREVIEWED$$sPUBLISHED
000170995 980__ $$aARTICLE