[Bioperl-l] TRANSFAC matrices, open acces

[Sendu Bala]

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.