User talk:Cchsieh

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How can I create a vitual gel electrophoresis map (in png or gif format)

If I had a DNA restriction cutting distance (length) in the array. just like:

         @EcoRI=(25.44, 24.31, 15.12, 11.02)
         @BamHI=(26.12, 15.34)
         @HindIII=(28.99)

How can I create a vitual graph (in png or gif format) in gel electrophoresis map? Which Perl modules should I choose for this purpose?

ThanX

  • I'm not sure. This is not the best place to ask, though. You should email the BioPerl mailing list; there may be someone else who can answer this. The mail list page also has the GMane link to search for past posts on the mail list. I also noticed the Graphics HOWTO has a quote about restriction maps (but no examples, sorry). --Chris Fields 15:35, 28 August 2006 (EDT)
    • Maybe I was wrong about the mail list suggestion! --Chris Fields 13:39, 29 August 2006 (EDT)
  • A long time ago I used VirtualPCR [1] program which draws very nice gels of 'virtual' PCR products. Maybe you can borrow some code to get what you want. --Mauricio 23:15, 28 August 2006 (EDT)
  • Bio::Tools::Gel can generate the gel band sizes for you from PCR product lengths (see the module page's linked documentation for more info). Just use something like GD to generate the gif.

References

  1. Lexa M, Horak J, and Brzobohaty B. Virtual PCR. Bioinformatics. 2001 Feb;17(2):192-3. PubMed ID:11238077 | HubMed [VirtualPCR]
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