IPknot

IPknot is a computational method for quickly predicting RNA secondary structures with pseudoknots that capture a broad range of pseudoknots. It decomposes a pseudoknotted structure into pseudoknot-free substructures and approximates a base-pairing probability distribution for predicting structures. A heuristic algorithm is also provided to refine base-pairing probabilities and improve accuracy. Integer programming with threshold cut is used to maximize expected accuracy. Additionally, IPknot can be extended to predict consensus secondary structures with pseudoknots from multiple sequence alignments.

Topic

Sequences;Structure prediction;RNA

Detail

  • Operation: Multiple alignment;Structure prediction;Alignment;RNA secondary structure prediction;Prediction

  • Software interface: Command-line user interface, we user interface

  • Language: Javascript;PHP;C++;Perl

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.0.0

  • Credit: Grant-in-Aid for Young Scientists (B) (KAKENHI) from Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, Global COE program 'Deciphering Biosphere from Genome Big Bang’ from MEXT, Japan, Grant-in-Aid for Scientific Research on Innovative Areas from MEXT, Japan.

  • Input: FASTA, CLUSTAL W

  • Output: -

  • Contact: Kengo Sato satoken@bio.keio.ac.jp

  • Collection: -

  • Maturity: Stable

Publications

  • IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
  • Sato K, et al. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. 2011; 27:i85-93. doi: 10.1093/bioinformatics/btr215
  • https://doi.org/10.1093/bioinformatics/btr215
  • PMID: 21685106
  • PMC: PMC3117384

Download and documentation

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