[Biojava-l] Retrieving Partial gene/CDS information

[Richard Holland]

Hello.

Whilst BioJava supports the < and > annotation, and will correctly load
these from the file and store them as FuzzyLocations internally, when it
is asked to write them to BioSQL they are lost. This is BioSQL has no
way of storing this information. Therefore when you save the sequence
into BioSQL and load it back in later, the < and > are lost.

cheers,
Richard

Bandaru, Sandya (NIH/NIAID) [C] wrote:
> Hi,
> 
> I used BioJava 1.6 to store Genbank sequences into MySQL database, and tried writing out the Sequence. I noticed the feature location is not having '<' or '>' (if is partial gene/CDS). I looked into the documentation of biojavax and didn't find way to get this information.
> 
> I found FuzzyLocation in Biojava. I appreciate if you can provide similar feature to get the partial CDS/gene locations.
> 
> Thanks to the BioJava team for the good work.
> 
> Regards,
> Sandya Bandaru
> Bioinformatics Software Developer
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 10401 Fernwood Road
> Bethesda, MD 20892
> 
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/