[Bioperl-l] GenBank ASN.1 SeqIO parser

Chris Mungall cjm at fruitfly.org
Thu Feb 7 21:14:20 EST 2008


Just to add to Barry's suggestions:

You can query the database directly:
http://www.berkeleybop.org/goose

You can also use the go-db-perl API and point it at the mysql port of  
one of the mirrors; see
http://www.geneontology.org/GO.database.shtml

On Feb 7, 2008, at 4:31 PM, Barry Moore wrote:

> 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
>>>>
>>>>
>>>>
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