RNAsnoop

RNAsnoop is a software tool that predicts the target nucleotides of orphan box H/ACA subclass small nucleolar RNAs (snoRNAs) using a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions. It is complemented by a support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information. The C source code of RNAsnoop is freely available for use.

Topic

Molecular interactions, pathways and networks;RNA;Nucleic acid structure analysis

Detail

  • Operation: Structured RNA prediction and optimisation

  • Software interface: Command-line user interface

  • Language: Perl

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: European Union under the auspices of the FP-6 SYNLET and the FP-7 QUANTOMICS project, the Austrian GEN-AU project ‘Regulatory Noncoding RNA’.

  • Input: -

  • Output: -

  • Contact: htafer@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • RNAsnoop: efficient target prediction for H/ACA snoRNAs.
  • Tafer H, et al. RNAsnoop: efficient target prediction for H/ACA snoRNAs. RNAsnoop: efficient target prediction for H/ACA snoRNAs. 2010; 26:610-6. doi: 10.1093/bioinformatics/btp680
  • https://doi.org/10.1093/bioinformatics/btp680
  • PMID: 20015949
  • PMC: -

Download and documentation


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