PLEXY: efficient target prediction for box C/D snoRNAs

• DOI: 10.1093/bioinformatics/btq642
• Publication Date: 2010-11-14T01:26:18Z
• Authors: Stephanie Kehr; Sebastian Bartschat; Peter F. Stadler; Hakim Tafer
• Keywords: Small nucleolar RNA; Nucleic acid structure

Abstract Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding with a wide variety cellular functions including chemical modification RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role box C/D snoRNAs is to determine the targets for 2′-O-ribose methylation, which important rRNA maturation splicing regulation some mRNAs. still unknown, however, many ‘orphan’ snoRNAs. While fast efficient target predictor H/ACA available, no comparable tool exists snoRNAs, even though they bind their much less complex manner. Results: PLEXY dynamic programming algorithm that computes thermodynamically optimal interactions snoRNA putative RNA. Implemented as scanner large input sequences equipped filters on duplex structure, reliable prediction sites. Availability: perl script freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY. Contact: [e-mail] Supplementary Information: data Bioinformatics online.