[Gmod-gbrowse] [Gmod-help] get a new GBrowse to work

[Peter]

On Tue, Sep 23, 2008 at 8:22 PM, Scott Cain <cain.cshl at gmail.com> wrote:
>
> Hi Zhiliang,
>
> (I cc'ed this to the gbrowse mailing list, since there may be advice
> or comments there on what course to take.)
>
> I haven't tried to use load_genbank.pl in a few years, so I can't say
> I'm surprised it doesn't work.  Its cousin script in BioPerl,
> bp_genbank2gff.pl, doesn't appear to load a Bio::DB::GFF database
> either, though it purports to.  I am currently of the opinion that the
> functionality you are looking for (providing a GenBank accession and
> having it loading into a GBrowse database) should be rewritten to use
> more "modern" technology: bp_genbank2gff3.pl and
> Bio::DB::SeqFeature::Store.  The SeqFeature::Store database is the one
> you'd want to use with GFF3.

Another option would be to setup a BioSQL database, and use one of the
Bio* projects (e.g. BioPerl) to import your GenBank files into it. GBrowse
can then be setup to read the BioSQL database (it uses BioPerl internally).

(This almost works fine for me - just a couple of GenBank files seem to
be causing me trouble, discussed on another thread on this mailing list.
Having more people using GBrowse with BioSQL should help!).

Peter