show motifs in GBrowse

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show motifs in GBrowse

Postby ABQ » Wed Mar 13, 2013 7:15 pm

Hello,
I would like to have some short DNA motif/sequences (at my wish) be graphically shown in the GBrowse, in a separate track. Well, it can be similar to the BLAST hit track, only my motifs are too short to go though the BLAST. I need this feature to visually estimate the frequency and location of given short motifs. Any idea how to make it happen?
Many thanks!
ABQ
 
Posts: 4
Joined: Wed Jan 25, 2012 4:49 pm

Re: show motifs in GBrowse

Postby Josh Goodman » Wed Mar 13, 2013 9:13 pm

I recommend you take a look at GBrowse 2.x that we just installed on Friday. It has better support for custom tracks and should let you do what you describe.

http://flybase.org/cgi-bin/gbrowse2/dmel/

See the tab labeled "Custom tracks".

Cheers,
Josh
Josh Goodman
Site Admin
 
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Joined: Mon Nov 26, 2007 2:39 pm


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