[Bioperl-l] Bio:DB:SeqFeature - MySql - Java

Bernd Jagla bernd.jagla at pasteur.fr
Mon Jan 11 05:11:16 EST 2010


Hi,

 

First off, I am not sure if this is supposed to be addressed to the Bioperl
or Gbrowse mailing list, so apologies if this is the wrong list and please
let me know.

 

I am writing a program in Java that needs to access genome annotation data.
Since I am using Gbrowse already I was thinking that I could combine both
approaches making life eventually easier for me. I am mainly interested in
getting a gene/feature name for a given position. The position is stored in
the feature table and through linking typelist, locationlist, (maybe
sequence), and feature I can get all the information I need. Unfortunately
it seems that the feature name is stored in the object blog of the feature
table. 

 

That is a bit suspicious to me because I don't understand why searching for
a name can be so fast if it is not indexed through mysql when searching
using GBrowse.

 

So my question is how to I parse the Bio::DB::SeqFeature object in JAVA
correctly to get the name of the feature and possible also any further
information.

 

Any suggestions are greatly appreciated. Maybe there is a better solution
than parsing Perl code with Java.?

 

Thanks a lot,

 

Bernd



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