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

skirov skirov at utk.edu
Tue Aug 22 14:12:59 EDT 2006


>===== Original Message From Chris Fields <cjfields at uiuc.edu> =====
>...
>> 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.
Correct. The format actually is a modification of swissprot, so I do not think 
they can claim it.
>
>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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