[Biojava-l] Can I get the additional information, such as chromosome number from "source" feature from genbank file?

pprun pzgyuanf at gmail.com
Sun Jul 19 14:26:05 UTC 2009

Thanks Richard for supplying this detail process.

Also nice to know you are still working back-stage of Biojava. :)


Richard Holland wrote:
> It's in the RichAnnotation object associated with the RichFeature inside
> the parsed RichSequence object (if you're using the BioJavaX
> GenbankFormat parser). The RichAnnotation is a key/value map - the keys
> are term objects, which you can find by requesting the term for
> "chromosome" from the default ontology. You can then search the map for
> the matching key/value pair.
> cheers,
> Richard
> On Sun, 2009-07-19 at 11:41 +0800, pprun wrote:
>>Given a genbank file with feature as this:
>>FEATURES             Location/Qualifiers
>>      source          1..412
>>                      /chromosome="12"
>>                      /map="12q22-qter"
>>                      /organism="Homo sapiens"
>>                      /db_xref="taxon:9606"
>>How can I get the chromosome="12" information? I need it to sort out the 
>>sequence by chromosome.
>>Appreciate your help.
>>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org

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