[Bioperl-l] Re: flybase release 4.2 gff

Don Gilbert gilbertd at bio.indiana.edu
Mon Sep 26 15:35:08 EDT 2005


The GFF  data from flybase is version 3 format, and at a quick look
the current 4.2 release is as valid  GFF3 as earlier 4.x releases. I
don't know what version of BioPerl added GFF3 support. I'm using 1.5.x
which will read the flybase release 4 GFF3 ok.

Did you have problems with just this recent dmel 4.2 release?

Though I'm no longer with the flybase project, the data dumper they
are  using is the one I wrote for dumping GMOD Bulkfiles from Chado
databases (and it works for other Chado databases). Find this software
at http://cvs.sourceforge.net/viewcvs.py/gmod/schema/GMODTools/

Sometime this will be packaged as a simpler-to-use Chado data dumper.
If this isn't producing proper GFF3 output, I'll be happy to correct

BTW, I've loaded dmel release 4.1 GFF into GBrowse v1.63
in multiple database adapators for tests.  Find configurations for 
D.melanogaster features in GBrowse at
  07.dmel_mysql.conf  == for MySQL database
  06.dmel_bdb.conf    == BerkelyDB database
  10.dmel_lucene.conf == Lucene database 
  05.dmel_lucegene.conf = Lucegene database 
Both of these Lucene adaptors  are as fast or faster than MySQL, and
you can copy the data indices and run locally with minimal setup, along with 
all the other Drosophila species annotations I've put up at
More info at

-- Don Gilbert

>From Michael Eisen mbeisen at lbl.gov
> Wed Sep 21 18:00:24 EDT 2005
> Has anyone written a script to convert flybases release 4.2 Drosophila 
> melanogaster annotations to gff suitable for bioperl?

Data from ftp://flybase.net/genomes/dmel/dmel_r4.2_20050909/gff/
##gff-version   3
##sequence-region       2L      1       22407834
#organism       dmel
#source FlyBase Chado DB r4.2.1
#date   20050807

$gbl/bin/bp_load_gff.pl --adaptor dbi::mysqlopt --user dgg 
  --dsn 'dbi:mysql:database=dmel_r42_20050909;host=localhost' 
  --create $w/dmel420/gffb/*gff.gz
/bio/argos/flybase/work.local/dmel420/gffb/dmel-2L-r4.2.1.gff.gz: loading...
/bio/argos/flybase/work.local/dmel420/gffb/dmel-2L-r4.2.1.gff.gz: 557362 records loaded

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/

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