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  • Yushan Hsiao
    Junior Member
    • Aug 2010
    • 6
    #1

    Any tools for RNA graph?

    I need to draw the secondary structure of small RNA precursors.
    Is there any tool that could produce many graphs at a time when I give it the all the sequences or parenthesis of RNAfold?

    Besides, I also want to mark the specific sequence on the graph of my RNA structure. I saw some paper with red letters on the graph to point them out, but I don't know how do they produce this result?

    Could anyone help? Thanks a lot.
    Tags: None
  • ppgardne
    Member
    • Oct 2010
    • 13
    #2
    VARNA is quite good. Lots of different layouts are possible.

    The Vienna package ships with RNAplot which will ps & svg. RNAfold usually generates a postscript (rna.ps) by default. There are some scripts for manipulating the Vienna ps files in your ViennaRNA-1.x.x/Utils/ directory.

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    • ppgardne
      Member
      • Oct 2010
      • 13
      #3
      R2R has just been published. It also produces some very nice graphics:
      http://www.biomedcentral.com/1471-2105/12/3

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