[Bioperl-l] TRANSFAC matrices, open acces

skirov skirov at utk.edu
Thu Jul 27 13:57:19 UTC 2006

Just a quick note- Bio::Matrix::PSM::IO can parse matrix.dat if you can get 
it- and as far as I can tell this is not easy- you have to contact the company 
to get access and it is not clear what their conditions are. This is the 
reason I have decided not to maintain the transfac parser.
>===== Original Message From Sendu Bala <bix at sendu.me.uk> =====
>Sean Davis wrote:
>> On 7/27/06 5:55 AM, "Sendu Bala" <bix at sendu.me.uk> wrote:
>>> Maximilian Haeussler wrote:
>>> Actually, the fact that the transfac matrices are belonging to a
>>> company is quite inconvenient for biologists and bioinformatics
>>> analyses working in this field.
> >
>>> The public version is adequate though. It would certainly be useful to
>>> have Bioperl access to transfac and other regulation databases. I'll
>>> probably write some suitable modules if no one beats me to it.
>> I haven't used it in a while, but the TFBS family of modules are, if I
>> recall correctly, bioperl-compatible, though not part of bioperl.  In any
>> case, for those who aren't aware, it might be worth a quick look:
>Yes. It only has online access to Transfac though, and the inheritance
>and returned objects are TFBS specific so you miss out on whatever
>goodness there may be in the rest of bioperl.
>Still, recommended to use if you want programmatic access to Transfac
>matrices right now.
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