title: PLEXY: efficient target prediction for box C/D snoRNAs.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY.
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany. steffi@bioinf.uni-leipzig.de
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kehr
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bartschat
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
mesh_terms: D000465:Algorithms; D012333:RNA, Messenger / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry; D020537:RNA, Small Nucleolar / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software; D013816:Thermodynamics
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar