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