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

Chris Fields cjfields at uiuc.edu
Tue Aug 22 14:31:42 EDT 2006


Hilmar,

No, unfortunately no TRANSFAC or similar matrices.  But there are a few
other similar resources out there that may provide matrices:

http://molbiol-tools.ca/DNA_Motifs.htm

This one allows you to create a matrix from input sequences:

http://molbiol-tools.ca/Jie_Zheng/


Chris

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Tuesday, August 22, 2006 1:04 PM
> To: Chris Fields
> Cc: 'Sendu Bala'; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] TFBS databases, Bio::Matrix::PSM suitable?
> 
> Good idea if that's feasible and not too difficult (or do they
> provide transfac format themselves?).
> 
> 	-hilmar
> 
> 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 




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