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

[Stefan Kirov]

Sam,
You can use MART to convert to ensembl id (in most cases). I don't think 
they support genebank. You can try to use genekeydb 
(genereg.ornl.gov/gkdb), either download it or use the online converter, 
but my guess is you are not going to get too many ids. One thing I may 
fix in the future, but right now... Still may be worth a try. Look at 
seqhound too (http://www.blueprint.org/seqhound/index.html).
Stefan

Brian Osborne wrote:

>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
>
>------ End of Forwarded Message
>
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>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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