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

Chris Fields cjfields at uiuc.edu
Sat Sep 9 18:35:25 EDT 2006


That should work for tests at least.  I don't know if the format has  
changed much (my guess is no).

Sendu seemed to be the one who was most interested taking this on.   
Sendu?

Chris

On Sep 9, 2006, at 4:03 PM, Maximilian Haeussler 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 :
>>> ===========================================================
>>>
>>>
>>>
>>
>>
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>>
>
>
>
> -- 
> Maximilian Haeussler,
> CNRS/INRA Gif-sur-Yvette, France
> tel: +33 6 12 82 76 16
> skype: maximilianhaeussler
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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