[Bioperl-l] Entrez Gene parser questions

Mingyi Liu mingyi.liu at gpc-biotech.com
Thu Jun 2 12:59:28 EDT 2005

Hi, Annie,

Stefan's more familiar with the requirements of entrezgene.pm.  Based on 
my experience installing entrezgene.pm for bioperl 1.5 (I don't have 
1.4) there's no need for a util.pm.  I suspect the reason why you 
mentioned a util.pm was that previously my Bio::ASN1::EntrezGene needed 
a util.pm, but that was eliminated since V1.02 or so and before 
Bio::ASN1 space was created on CPAN.  Maybe Stefan had not updated the 
documentation to reflect this change?

You do need to install Bio::ASN1::EntrezGene first, then copy both the 
entrezgene.pm and the latest Bio::Annotation::DBLink from bioperl CVS 
since entrezgene.pm uses the url() in DBLink, which is not present in 
even bioperl 1.5.  For me, I also had to do a force install 
Grapha::Directed, but that might not be a problem for you if your system 
already has it (my bioperl installation was old and incomplete before).



Law, Annie wrote:

>I would appreciate help with the following.  First of all, I would like to say it's great that a Entrez gene parser was written. I just have some questions to get me started.  
>A) I already have bioperl 1.4 installed.  I would like to know if I can install the Entrez gene parser and 
>Stefan Kirov's entrezgene.pm with out reinstalling bioperl.  If this is not advised then I would reinstall bioperl.
>I was going to 1. install the Bio::ASN1::EntrezGene module (perl Makefile.PL, make, make test, make install, etc...)
>		   2. just take only the entrezgene.pm and util.pm file and put it in the appropriate directory
>               (which util.pm shold I use??  I searched CPAN and got many results for util.pm
>               is it Biblio::Util, Boulder::Util, or something else??)
>B) For each Entrez gene id how do I access the associated Unigene id, accession numbers, gene symbol, gene name,
>And GO IDs.  
>Also, I have been looking at the code and the POD within it.  Are there some other places that I can look for documentation?
>Thanks so much!!
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

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