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

Chris Fields cjfields at uiuc.edu
Sat Sep 9 19:29:17 EDT 2006


One of the requests that may pop up is having your modules be  
backwards compatible with older TRANSFAC files, especially since the  
new ones are not publicly available.  Don't know how easy that would  
be since, as you say, the formats have changed quite a bit...

Chris

On Sep 9, 2006, at 6:03 PM, Sendu Bala wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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