PLEXY: efficient target prediction for box C/D snoRNAs

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.

[1]  Liang-Hu Qu,et al.  Exploration of pairing constraints identifies a 9 base-pair core within box C/D snoRNA-rRNA duplexes. , 2007, Journal of molecular biology.

[2]  Valery Shepelev,et al.  snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. , 2008, Gene.

[3]  Mihaela Zavolan,et al.  The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. , 2010, Human molecular genetics.

[4]  Christian M. Reidys,et al.  Partition function and base pairing probabilities for RNA-RNA interaction prediction , 2009, Bioinform..

[5]  Peter F. Stadler,et al.  RNAsnoop: efficient target prediction for H/ACA snoRNAs , 2010, Bioinform..

[6]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[7]  Hakim Tafer,et al.  RNAplex: a fast tool for RNA-RNA interaction search , 2008, Bioinform..

[8]  Laurent Lestrade,et al.  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs , 2005, Nucleic Acids Res..

[9]  S. Stamm,et al.  The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.

[10]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[11]  Dmitry A. Samarsky,et al.  A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae , 1999, Nucleic Acids Res..

[12]  R. Terns,et al.  Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. , 2002, Gene expression.

[13]  Peter F. Stadler,et al.  Partition function and base pairing probabilities of RNA heterodimers , 2006, Algorithms for Molecular Biology.