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

[Ewan Birney]

hz5 at njit.edu wrote:
> http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp
> 
> Quoting Stefan Kirov <skirov at utk.edu>:
> 
>> 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,
>>


I know this is rather old, but at Ensembl we do, of course, track GenBank
accession numbers - these are the identifiers shared with EMBL. We don't
track GenBank gi numbers as they are too volatile.


>> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
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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
>>
>> "And the wars go on with brainwashed pride
>> For the love of God and our human rights
>> And all these things are swept aside"
>>
>> _______________________________________________
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>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 
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