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

Stefan Kirov stefan.kirov at bms.com
Fri Nov 30 11:12:22 EST 2007


Chris Fields wrote:
> 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).
>   
Yes, I think this would be a good step.
Stefan
> 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.
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>         
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
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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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