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

[Cook, Malcolm]

we use TFBS all the time against data coming from a recent local install of TRANSFAC(r) Professional 11.1 (2007-03-31)

the most recent is 11.4 (2007-12-14)

TFBS::* has the nice advantage that you can interoperate Transfac pwms with other (say, Jaspar) matrices and/or simple consesus sequence patterns; and it COULD be fairly easily extended to allow interoperation with other sources, say cisRED.  "One interface to rule them all" - bwa ha ha.

However, if you DO have locally installed Transfac (Pro) ($$), and want to use just it, then you should know that you can also call their `match` routines from the unix command line (though this is not documented to my knowledge).  I can supply my cheat sheet or otherwise advise if desired.  Also, if you go this way, I've written the requisite TFMatchOut2GFF to convert TRANSFAC match's output to GFF, if it suits your purpose, which I could release if asked.

If you want to use TFBS::**, I have written a command-line wrapper for the TFBS perl modules that might give you a leg up if you decide to use TFBS::**.  I could release them too, if useful.

But I agree, if I recall, TFBS::* were dropped from ongoing active development due to issues with data access policys.  And, I think that they no longer with with remotely hosted Transfac.  They did a few years ago. I think I tested a while ago and found that they do not.

Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Thursday, March 06, 2008 9:42 AM
> To: Sean Davis
> Cc: bioperl-l at lists.open-bio.org; Edward Wijaya
> Subject: Re: [Bioperl-l] BioPerl Module to Parse Transfac
> Flat File Database
>
> 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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