[From nobody Tue Apr 17 13:24:39 2007
Date: Tue, 17 Apr 2007 10:30:11 -0400
From: Stefan Kirov <stefan.kirov@bms.com>
Subject: Re: [Bioperl-l] How to Create Sequence and TFBS Graph with Perl
In-reply-to: <462473B7.4070905@i2r.a-star.edu.sg>
To: Edward WIJAYA <ewijaya@i2r.a-star.edu.sg>
Message-id: <4624D9F3.5050805@bms.com>
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References: <462473B7.4070905@i2r.a-star.edu.sg>

I believe you can use Bio::Graphics for this. I have done so in the past 
and I find it quite straightforward.
You can use the imagemap option to create annotation (mouseovers and 
links) for different hits. Also with a little bit of javascript you can 
create selectors to display different images/imagemaps based on the 
Bio::Graphics output. There is a lot of documentation out there for 
Bio::Graphics.
This can get you started:
http://stein.cshl.org/genome_informatics/BioGraphics/index.html
The example is with BLAST, but you can use it for TFBS as well.
Also dig the perl docs for image maps to make the figure interactive.
Hope this helps,
Stefan

Edward WIJAYA wrote:
> Dear all,
>
> How do you usually construct a graph for TFBS (binding sites) position
> within their sequences? I was thinking to build something like this kind of
> visualization tool:
>
> http://research.i2r.a-star.edu.sg/Dragon/Motif_Search/cgi-bin/tmp/29740M1.html
>
> or
>
> http://wingless.cs.washington.edu:8080/assessment/servlet?filenameID=submission/SPACE.D9F26D506DE90E9A0A0010BB6BCCAEF3&pageType=visualizationForm&action=Visualize+It
>
> Is there a BioPerl module to do that?
>
> --
> Edward
>
>
>
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