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

Jonathan Epstein Jonathan_Epstein at nih.gov
Tue Jul 20 17:53:00 UTC 2010


Hi,

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 
environment.


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


Thanks in advance for your guidance,

Jonathan








More information about the Bioperl-l mailing list