[Bioperl-l] BioPerl Module to Parse Transfac Flat File Database

[Sendu Bala]

Sean Davis wrote:
> On Thu, Mar 6, 2008 at 8:07 AM, Sendu Bala <bix at sendu.me.uk> wrote:
>> Edward Wijaya wrote:
>>  > Dear experts,
>>  >
>>  > Is there any? The TRANSFAC text file which contain entry like this.
>>  > Especially we wich to capture the PWM for each of the Transcription
>>  > factor.
>>
>>  Yes; I've written a module to do this, I just haven't committed it yet
>>  because certain things aren't quite right in terms of the API. But to
>>  just grab the PWM it should work fine. If you want I can email you the
>>  modules.
> 
> I believe there are a set of non-bioperl modules called TFBS.  See
> here (although I'm not sure this is the most up-to-date site):
> 
> http://tfbs.genereg.net/

I believe it's out of date enough to not work on the latest Transfac 
data, though I haven't used tried to confirm.

At any rate, the Transfac (Pro) database is pretty strange and 
complicated, and the TFBS modules certainly don't let you access 
everything in the way you might want or expect.