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Gene Fusion in DNA data

by ZWcarp (Beadle)
on Oct 13, 2011 at 20:41 UTC ( #931379=perlquestion: print w/replies, xml ) Need Help??
ZWcarp has asked for the wisdom of the Perl Monks concerning the following question:

Hello Monks, I was wondering if anyone was aware of any modules or scripts that have been (or are being) developed for detecting gene fusion events in DNA sequencing data. Even any reference to literature or anything relevant would be helpful I really don't want to start from scratch on this one. Thanks!

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Re: Gene Fusion in DNA data
by toolic (Bishop) on Oct 13, 2011 at 21:03 UTC
      http://soap.genomics.org.cn/SOAPfusion.html Have fun! Mark. MISCB.
Re: Gene Fusion in DNA data
by BioLion (Curate) on Oct 18, 2011 at 09:19 UTC

    This is a pretty complex question, but detection usually depends on clever ways of aligning your sequence to the reference genome and then fishing for events that are not 'normal', i.e. all those that can only be explained by fusion events etc...

    I don't know of any dedicated (Perl) code for this, but perl is certainly capable of doing the filtering.

    You might be better asking at a more specific forum e.g. seqAnswers or cruising the literature on pubmed.

    Happy hunting!

    Just a something something...

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[Corion]: choroba: I'm still using spod5 as my pod-to-ooxml- converter didn't really get off the ground so far
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[Corion]: choroba: spod5 converts pod to S5 HTML, so it's also still basic. I find the lack of animations (in the sense of "highlight this", "highlight that" in code) somewhat tedious as I do it with rendered PNGs
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[Corion]: Doing that in Powerpoint or Ooxml would be nice(r) but I'm much quicker doing the outline of a presentation and the code as Pod

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