[Bioperl-l] TRANSFAC matrices, open acces

[Remo Sanges]

Here is also my 2c on TFBS:

skirov wrote:

>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.
>Stefan
>  
>
>>===== 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
>>

TFBS::DB::LocalTRANSFAC - can parse local
transfac matrices (matrix.dat)

>>, and the inheritance
>>and returned objects are TFBS specific so you miss out on whatever
>>goodness there may be in the rest of bioperl.
>>
>>    
>>

In TFBS there are modules which inherithed
from Bio::SeqFeature::Generic and
Bio::Root::Root.
See for example TFBS::Site.

So probably it is not so bad....
Here is the link cutted from the Sean's e-mail:

http://forkhead.cgb.ki.se/TFBS/

HTH

Remo