[Bioperl-l] TFBS databases, Bio::Matrix::PSM suitable?

Sendu Bala bix at sendu.me.uk
Sat Sep 9 19:03:16 EDT 2006


Chris Fields wrote:
> That should work for tests at least.  I don't know if the format has 
> changed much (my guess is no).  
> 
> Sendu seemed to be the one who was most interested taking this on.  Sendu?

Yes, I'm currently working on this. Well, I've finished really, but am 
doing related things now before I commit. Regarding tests, its not just 
the matrix.dat file that I'm working with. 
http://biotech.embl-ebi.ac.uk:8400/sw/common/test/ does have a few of 
the other files, but for the ones I've looked at the format has changed 
significantly enough that they're not really useful.

I'm still waiting for a reply from their support, but worst case I can 
just make some files in the correct format but with gibberish data.


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