[Bioperl-l] How to Create Sequence and TFBS Graph with Perl

Stefan Kirov stefan.kirov at bms.com
Thu Apr 19 14:01:28 EDT 2007


I will see if I can post it or perhaps commit something to the bp 
scripts. In any case it won't be before Monday- I have deadlines to meet.
Stefan
Edward WIJAYA wrote:
>
> Hi Stefan,
>> I believe you can use Bio::Graphics for this. I have done so in the 
>> past and I find it quite straightforward.
> Do you still have that sample script? I don't find it simple to do.
> I was thinking of doing something like this:
>
> http://nar.oxfordjournals.org/content/vol31/issue13/images/large/gkg56702.jpeg 
>
>
> Appreciate if you can share it with us.
>
> -- 
> Edward
>
>
>>
>>
>> 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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>>
>>
>
>
>
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