[Bioperl-l] GenBank ASN.1 SeqIO parser

Ryan Golhar golharam at umdnj.edu
Thu Feb 7 18:04:50 EST 2008


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.
>>>
>>> _______________________________________________
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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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