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genome GFF to BioMart tool (alpha)

Dear Genome miners,

Find this tool of interest if you have piles of genome GFF annotations
that you want a better way to sift through:

gff2biomart.pl -- create tables for BioMart from genome GFF annotations

The script generates table .sql, .txt and .xml suited to BioMart
(MySQL, BioMart version 0.3 tested). It is a simple script without
special requirements, basically a data transformer that writes new
files formatted for a BioMart database.

-- filter (include,exclude) features that exist in regions, including
joint filters (has homology to human but not to fly or worm genes; has
predicted gene but not homology; any such feature type comparison).
-- output 4 kinds of attributes: a feature table, per-feature sequence,
region table, per-region sequence.

Please have installed and used BioMart before trying to load the outputs
of this.

EXAMPLE BioMart : DroSpeGe
BioMart : DroSpeGe provides a tool for mining homologies and
annotations of [twelve] Drosophila species genomes.
You can select genome regions with the available annotations, and
exclude others, and download tables or sequences of the selection
set. For instance, select the regions with Mosquito gene homologs,
but no D. melanogaster gene homologs. Or select regions with
gene predictions but no known homolog.

DroSpeGe's BioMart is built with the GMOD Tool gff2biomart.pl
Example data sets from this tool are at

This is a alpha-level, not yet fully tested.
This will be part of a GMODTools release. Find the pre-release script at
http://eugenes.org/gmod/GMODTools/ or at GMOD.sf.net CVS schema/GMODTools/

- Don Gilbert

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

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Don Gilbert <gilbertd@bio.indiana.edu>

Posted by Scott Cain 2006-01-12