FW: [Bioperl-l] How to extract promoter region seq from genbank or
brian_osborne at cognia.com
Fri Oct 14 21:28:56 EDT 2005
------ 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
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.
Brian Osborne <brian_osborne at cognia.com> wrote:
> 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
> 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
>> > 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
Sam Al-Droubi, M.S.
saldroubi at yahoo.com
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