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

[Stefan Kirov]

My bad Ewan. I was looking for Genbank in external_db, did not see it 
and assumed you don't keep Genbank... Sorry.
Stefan

Ewan Birney wrote:

>
>
> 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
>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>  
>>>>
>>> -- 
>>> 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"
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> =========================================================
>> Haibo Zhang, PhD
>> Computational Biology
>> http://www.cyberpostdoc.org/
>> Share postdoc information in cyberspace. Welcome your stories, 
>> suggestions and advice!
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--