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Media type:
E-Article
Title:
PLEXY: efficient target prediction for box C/D snoRNAs
Contributor:
Kehr, Stephanie;
Bartschat, Sebastian;
Stadler, Peter F.;
Tafer, Hakim
Published:
Oxford University Press (OUP), 2011
Published in:
Bioinformatics, 27 (2011) 2, Seite 279-280
Language:
English
DOI:
10.1093/bioinformatics/btq642
ISSN:
1367-4811;
1367-4803
Origination:
Footnote:
Description:
Abstract Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D snoRNAs is to determine the targets for 2′-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many ‘orphan’ snoRNAs. While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner. Results: PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C/D snoRNA target sites. Availability: The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY. Contact: steffi@bioinf.uni-leipzig.de Supplementary Information: Supplementary data are available at Bioinformatics online.