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

Maximilian Haeussler maximilianh at gmail.com
Tue Sep 12 12:21:05 EDT 2006


FYI: I knew that there was an older version, finally found it on the
emboss mailing list:
http://newportal.open-bio.org/pipermail/emboss/2005-August/002178.html
They refer to:
ftp://ftp.ebi.ac.uk/pub/databases/transfac/
That is version 3.4 that I mentioned. There are quite a few matrices
and sites in there.

cheers,
Max

On 09/09/06, Maximilian Haeussler <maximilianh at gmail.com> wrote:
> (just found this old mail, sorry for the delay, reading too many mailing
> lists, how many hours do you guys spend on reading mailng lists per day???)
>
> Transfac versions 3.4 and 4.0 (If I remember well) had a much more open
> licence, at that time you were still allowed to download and distribute the
> file (you can still find these old versions on the net, e.g.
> http://biotech.embl-ebi.ac.uk:8400/sw/common/test/matrix.dat).
> I guess an older version could be used for the test cases in Bioperl.
>
> Another argument for supporting the transfac format in Bioperl is that it is
> the only de-facto standard format for matrices. Many pwm scanners and
> websites can parse it or at least supply a converter for Transfac into their
> own format.
>
> cheers,
> Max
>
>
>
> On 22/08/06, Chris Fields <cjfields at uiuc.edu> wrote:
> > 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 :
> > >
> ===========================================================
> > >
> > >
> > >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> Maximilian Haeussler,
> CNRS/INRA Gif-sur-Yvette, France
> tel: +33 6 12 82 76 16
> skype: maximilianhaeussler


-- 
Maximilian Haeussler,
CNRS/INRA Gif-sur-Yvette, France
tel: +33 6 12 82 76 16
skype: maximilianhaeussler


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