[Bioperl-l] best method for dealing with hg18 seq-features in a relational database?

Jonathan Epstein Jonathan_Epstein at nih.gov
Tue Jul 20 13:53:00 EDT 2010


I need a reasonably rapid runtime method to extract the gene features 
associated with a particular genomic region in the hg18 human assembly.  
This seems to require a relational database.  Of course I would like to 
do this using Bioperl.

So then the question becomes: what's the best approach to use?  
Biosql/BioPerl-db looks like the cleanest solution, but it's not clear 
to me how up-to-date it is; it sort of looks like an abandoned project.

CHADO/Gmod is more actively maintained, but I don't know how/whether I 
can obtain BioPerl bindings.

I am also open to using the UCSC databases as a starting point, since 
I've already mirrored most of the human-related portions of the UCSC 

Then there's the small matter of loading the hg18 annotations into the 
appropriate relational database.

Thanks in advance for your guidance,


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