PLEXY

The software tool PLEXY is a dynamic programming algorithm designed to predict target sites for box C/D snoRNAs, which play an important role in rRNA maturation and splicing regulation of some mRNAs. PLEXY computes thermodynamically optimal interactions between a snoRNA and a putative target RNA and includes filters on the duplex structure for efficient and reliable prediction. The tool fills a gap in available target predictors for orphan snoRNAs and provides a valuable resource for understanding the function of these non-coding RNAs.

Topic

Structure prediction

Detail

  • Operation: RNA secondary structure prediction

  • Software interface: Command-line user interface

  • Language: Perl;

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: European Union under the auspices of the FP-7 QUANTOMICS project.

  • Input: FASTA

  • Output: -

  • Contact: Stephanie Kehr steffi@bioinf.uni-leipzig.de

  • Collection: -

  • Maturity: -

Publications

  • PLEXY: efficient target prediction for box C/D snoRNAs.
  • Kehr S, et al. PLEXY: efficient target prediction for box C/D snoRNAs. PLEXY: efficient target prediction for box C/D snoRNAs. 2011; 27:279-80. doi: 10.1093/bioinformatics/btq642
  • https://doi.org/10.1093/bioinformatics/btq642
  • PMID: 21076148
  • PMC: -

Download and documentation

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