FW: [Bioperl-l] How to extract promoter region seq from genbank or another source?

[Brian Osborne]

ENSEMBL experts?

------ Forwarded Message
From: Sam Al-Droubi <saldroubi at yahoo.com>
Date: Fri, 14 Oct 2005 14:05:38 -0700 (PDT)
To: Brian Osborne <brian_osborne at cognia.com>
Subject: Re: [Bioperl-l] How to extract promoter region seq from genbank or
another source?

Hi Brian,
 
Thank you for the response.  I looked at it but it seems that enembl does
not use accession numbers.   It seems that they have their own numbering
scheme.  If so how do I get the mapping between the two.  If I can't get the
promoter region sequence then do you know if there is a way I can get the
entire chromosome sequence?  If so, I can then try to find the gene within
it and then grab the promoter region.
I am new to all this so I am sorry if I sound ignorant in this area.
 
On the surface, it seems that one should be able to do this easily but it
has not been easy so far.
 
Thank you. 


Brian Osborne <brian_osborne at cognia.com> wrote:
> Sam,
> 
> ensembl may be one solution, I think it provides a good API for these sorts
> of queries. See the ensembl API documentation for more information
> (http://www.ensembl.org/info/software/core/core_tutorial.html).
> 
> Brian O.
> 
> 
> 
> On 10/13/05 11:25 AM, "Sam Al-Droubi" wrote:
> 
>> > Hello,
>> > 
>> > I am totally new to BioPerl. I was able to install it and retrieve data
>> from
>> > GenBank. I have a list of accession numbers for genes but I want to use
>> > BioPerl to get the promoter region (1000 bp before the start of the gene).
>> > Can someone point me in the right direction on how to accomplish this.
>> > 
>> > Tech info: Using bioperl-1.5 on SuSE 9.3 professional machine.
>> > 
>> > Thank you.
>> > 
>> > 
>> > 
>> > 
>> > Sincerely, 
>> > Sam Al-Droubi, M.S.
>> > saldroubi at yahoo.com
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at portal.open-bio.org
>> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> 


Sincerely, 
Sam Al-Droubi, M.S.
saldroubi at yahoo.com

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