[Bioperl-l] GenBank ASN.1 SeqIO parser

Barry Moore barry.moore at genetics.utah.edu
Thu Feb 7 19:31:53 EST 2008


Ryan,

I you have a list of NCBI Gene IDs then you can grab the flatfile  
gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
gene2go.gz.  That will give you tax_id, gene_id, go_id, evidence  
code, qualifier, category etc.  From there  you can get the  
description from the GO OBO file http://www.geneontology.org/ontology/ 
gene_ontology_edit.obo.  If all you need is the description then the  
file is pretty easy to parse on the fly, but if you need to traverse  
the graphs or if you want an already written parser then add go-perl  
http://search.cpan.org/~cmungall/go-perl/go-perl.pod

Barry



On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote:

> Let me re-phrase then - I want to parse an entry such as this:
>
> http://www.ncbi.nlm.nih.gov/sites/entrez? 
> db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258
>
> to retrieve the text of the Gene Ontology entries and the  
> associated GO
> IDs for those entries.  Is this possible with BioPerl?  If so, how  
> can I
> do this with BioPerl?
>
> Ryan
>
>
>
> Jason Stajich wrote:
>> ugh - why parse ASN.1? NCBI provides converter application in the  
>> ncbi
>> toolkit to many formats : genbank, XML, etc.
>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote:
>>
>>> No.  The only ASN.1 parser is entrezgene.  You could probably try
>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses
>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences:
>>>
>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ 
>>> Bio/ASN1/Sequence.pm
>>>
>>>
>>> chris
>>>
>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote:
>>>
>>>> Is there a SeqIO parser module for GenBank ASN.1 format?  I thought
>>>> it would have been genbank or entrezgene, but neither of them work.
>>>>
>>>> _______________________________________________
>>>> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list