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K2N
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K2N

K2N is a tool that provides several different algorithms to remove pseudoknots to make knotted RNA structures to nested structures.



K2N

K2N is a tool that provides several different algorithms to remove pseudoknots to make knotted RNA structures to nested structures.

Topic

RNA; Nucleic acid structure analysis; Software engineering; Structure prediction; Gene transcripts

Details

  • Operation: RNA secondary structure prediction; Structure visualisation; RNA structure prediction; RNA structure covariance model generation
  • Software interface: Web user interface
  • Language: Python
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
    • Cost: Free
  • Version name: -
  • Credit: The Centre for Medical Systems Biology; the Netherlands Genomics Initiative, funded by the Dutch government.
  • Contact: ibivu _at_ few.vu.nl | rob _at_ spot.colorado.edu | Sandra Smit S.Smit _at_ few.vu.nl
  • Collection: -

Publications

Smit S, Rother K, Heringa J, Knight R "From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal." RNA 2008; 14(3):410-6 https://doi.org/10.1261/rna.881308
PMID: 18230758
PMCID: PMC2248259


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