[Bioperl-l] GenBank ASN.1 SeqIO parser

Chris Fields cjfields at uiuc.edu
Thu Feb 7 18:39:11 EST 2008


Bio::SeqIO::entrezgene should do this.  Any dbxrefs (including GO IDs)  
should be stored in the annotation collection, but I'm not sure how it  
is parsed; you'll have to test it out.

I agree with Jason; ASN.1 isn't a very friendly format.  Don't know  
why NCBI sticks with it, but I'm sure they have their reasons (I think  
this may have been discussed before on the list).

chris

On Feb 7, 2008, at 5:04 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.
>>>>
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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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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