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

Robert Buels 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.

perldoc Bio::DB::SeqFeature::Store.

 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:
> 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
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