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

Hilmar Lapp hlapp at gmx.net
Tue Aug 22 14:04:05 EDT 2006

Good idea if that's feasible and not too difficult (or do they  
provide transfac format themselves?).


On Aug 22, 2006, at 1:20 PM, Chris Fields wrote:

> ....
>> I've sent an email to their support address (though this may take  
>> a long
>> time to get a reply to, going on past experience).
>> This is the full legal spiel they have:
>> http://www.gene-regulation.com/pub/databases/transfac/doc/misc.html
>> There's nothing about restrictions on using the data format, they
>> haven't tried to shut down the TFBS:: modules, and it would be  
>> illegal
>> for them to do so according to fair use in many countries, their home
>> country of Germany especially. In short, the module itself would  
>> not be
>> a problem. The only cause for concern is the test data, which is not
>> possible without express permission. I've asked for permission so  
>> now we
>> just wait.
> Based on that you could proceed.  As long as the format itself isn't
> restricted you could create 'foo' data for the time being for tests.
> You might use some of the data from George Church's E. coli work  
> converted
> to TRANSFAC format and matrices (just reference it if you do); I  
> believe
> this is public domain (the data has been published).  Most of these  
> are in
> the form of alignments only:
> http://arep.med.harvard.edu/ecoli_matrices/
> Chris
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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