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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Fri Nov 30 12:01:29 EST 2007


I'm Cc'ing Mingyi Liu in this so he can know about your proposal (in the 
past, he mentioned he doesn't track the list closely).

Mauricio.

Stefan Kirov wrote:
> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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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>>   
> 
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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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