[Bioperl-l] Reading GenBank Genomic File Annotation

[Brian Osborne]

Nick,

This is from the HOWTO:

Another way of describing a feature in Genbank involves multiple start and
end positions. These could be called "split" locations, and a very common
example is the join statement in the CDS feature found in Genbank entries
(e.g. join(45..122,233..267)). This calls for a specialized object,
Bio::Location::SplitLocationI, which is a container for Location objects:

      for my $feature ($seqobj->top_SeqFeatures){
        if ( $feature->location->isa('Bio::Location::SplitLocationI')
                       && $feature->primary_tag eq 'CDS' )  {
            for my $location ( $feature->location->sub_Location ) {
                print $location->start . ".." . $location->end . "\n";
          }
        }
      }



Brian O.


On 5/19/06 2:12 PM, "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
wrote:

> Specifically: 
> I have the document to which you refer,
> but have not seen this one thing I need in the printout of tags etc.:
> the values in this line;
>      mRNA            join(380..509,578..1913,7784..8649,9439..10200)
> Is that a  location object?
> 
> 
> 
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
> 
> 
>> ----------
>> From:  Brian Osborne
>> Sent:  Thursday, May 18, 2006 5:54 PM
>> To:  Staffa, Nick (NIH/NIEHS) [C]; bioperl-l at lists.open-bio.org
>> Subject:  Re: [Bioperl-l] Reading GenBank Genomic File Annotation
>> 
>> Nick,
>> 
>> Have you read the Feature-Annotation HOWTO? This would be a good starting
>> point...
>> 
>> Brian O.
>> 
>> 
>> On 5/18/06 4:49 PM, "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov>
>> wrote:
>> 
>>> Would like a fairly simple way to extract certain information from Genbank
>>> Genomic File Annotations.
>>> Namely the six D.melanogaster sequences.
>>> Specifically to find gene entries and learn the gene name, begin and end and
>>> CDS.
>>> Please point me to appropriate modules and documentation.
>>> 
>>> 
>>> Nick Staffa
>>> Telephone: 919-316-4569  (NIEHS: 6-4569)
>>> Scientific Computing Support Group
>>> NIEHS Information Technology Support Services Contract
>>> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
>>> National Institute of Environmental Health Sciences
>>> National Institutes of Health
>>> Research Triangle Park, North Carolina
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
> 
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