[Bioperl-l] Collecting genomic DNA sequences using Entrez IDs

Chris Fields cjfields at uiuc.edu
Fri Nov 30 10:47:32 EST 2007


My bad.  I always forget about Bio::ASN1::Entrezgene.  We should ask  
Mingyi Liu if he would like to include this parser with BioPerl (since  
it requires it, makes sense to me, and it avoids the circular  
dependency that has plagued these modules).

chris

On Nov 30, 2007, at 9:29 AM, Stefan Kirov wrote:

> Chris Fields wrote:
> Chris,
> Bio::SeqIO::entrezgene requires Bio::ASN1::Entrezgene, which is the
> low-level parser and is not part of bioperl. There is a circular
> dependency- Bio::ASN1::Entrezgene depends on Bio::SeqIO (I think)....
> Paul, you can get it from CPAN and this should make
> Bio::SeqIO::entrezgene functional for you.
> Stefan
>
>
>> Bio::DB::EntrezGene and Bio::SeqIO::entrezgene are part of bioperl-
>> core (I think they were added prior to the 1.5.1 release, but I'm not
>> positive).  If possible you should try installing bioperl 1.5.2 or  
>> the
>> latest code from CVS.
>>
>> For directions on installing Bioperl for most OS's go here:
>>
>> http://www.bioperl.org/wiki/Installing_BioPerl
>>
>> From CVS:
>>
>> http://www.bioperl.org/wiki/Using_CVS
>>
>> chris
>>
>> On Nov 28, 2007, at 7:20 PM, Paul N. Hengen wrote:
>>
>>
>>> Hi.
>>>
>>> I have a number of gene IDs from Entrez and I want to find the
>>> start and end locations in the human genome. This seemed simple
>>> enough, so I started working through some of the examples for
>>> using the EntrezGene module at www.bioperl.org  Of course this
>>> did not work because the core installation does not include this
>>> module. So, I think I have two choices (1) install the module  
>>> (how?),
>>> or (2) find an easier way to get the locations in the human genome.
>>> I want to use the locations to grab sequences out of the genome.
>>> Can anyone offer advice on this? Thanks.
>>>
>>> -Paul.
>>>
>>> --
>>> Paul N. Hengen, Ph.D.
>>> Hematopoietic Stem Cell and Leukemia Research
>>> City of Hope National Medical Center
>>> 1500 E. Duarte Road, Duarte, CA 91010 USA
>>> mailto:paulhengen at coh.org
>>>
>>> -- 
>>> View this message in context: http://www.nabble.com/Collecting-genomic-DNA-sequences-using-Entrez-IDs-tf4894403.html#a14017289
>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>>
>>> _______________________________________________
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>>> Bioperl-l at lists.open-bio.org
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>>>
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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>>
>>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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