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

Hilmar Lapp hlapp at gmx.net
Tue Aug 22 10:36:34 EDT 2006

On Aug 22, 2006, at 8:18 AM, Sendu Bala wrote:

>> Transfac is not an open database so, you cannot get the instance data
>> anyway.
> You can. It is in the sites.dat file and often in the matrix.dat file.
> It is also available freely and publicly via at least 2 websites.

 From the Biobase website:

The TRANSFAC Public database is available at www.gene-regulation.com.  
This less maintained and data reduced version is free-of-charge. It  
is available for online use only, downloads are not available.

I will bet that every site offering transfac for download for free is  
in breach of the Biobase license unless they have an explicit  
agreement to do so with Biobase (which would be very surprising  
giving the language at their site).

We have had a site being quoted here a couple weeks ago and within a  
day of that they've had their downloads removed from their website,  
presumably because they received a call from a Biobase attorney.

If you know sites that offer transfac for download, please quote them  
here, presuming that they do so legally.

>> There was a discussion on that recently. Since Bioperl is
>> completely open project, I am not sure it makes sense to put efforts
>> into supporting something that is not open- even if you have  
>> access to
>> the data files (which I believe Transfac does not allow in general)
> It does allow it; you just have to pay for fast access to the latest
> data. Or you can use older data for free via the web. A Bio::DB module
> could provide access to either.

That is correct, and that could be very valuable.

>> how the rest of us can use it or debug/support it?
> It may be possible to include a small example subset of the data in
> t/data; there is after all already t/data/transfac.dat (which is a  
> small
> matrix.dat file).

I will check that file and any other transfac data that get uploaded  
to the repository; if it appears to be in breach of the Biobase  
license I will remove it.


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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