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

Chris Fields cjfields at uiuc.edu
Tue Aug 22 13:20:48 EDT 2006


....
> 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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