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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.

    Comment

    • ppgardne
      Member
      • Oct 2010
      • 13
      #3
      R2R has just been published. It also produces some very nice graphics:
      R2R - software to speed the depiction of aesthetic consensus RNA secondary structures - BMC Bioinformatics
      http://www.biomedcentral.com/1471-2105/12/3
      Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

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