[Bioperl-l] best method for dealing with hg18 seq-features in a relational database?
rmb32 at cornell.edu
Tue Jul 20 14:42:36 EDT 2010
Take a look at Bio::DB::SeqFeature::Store. It's got a loader that ships
with bioperl, bp_seqfeature_load.pl.
From the sound of it, the GMOD/Chado stuff might be too heavyweight for
what you are doing. But a good method for accessing a Chado schema from
Perl is Bio::Chado::Schema,
http://search.cpan.org/perldoc?Bio::Chado::Schema, which is based on
Hope this helps!
Jonathan Epstein wrote:
> 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,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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