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

Stefan Kirov stefan.kirov at bms.com
Fri Nov 30 10:29:57 EST 2007


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