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

[Stefan Kirov]

Sendu Bala wrote:
> 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 I believe it's out of date enough to not work on the latest Transfac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.
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Also be careful: there is a difference between PFM and PWM. Getting PWM
through most programs I have encountered will assume random distribution
(0.25 per each position in the background), unless you specify your own.
This could be something you may be comfortable with, but you definitely
should be aware of.