Date: 23 Oct 1999 http://www.fruitfly.org/seq_tools/datasets/Drosophila


This directory contains a set of GenBank flat-file format entries of
multiple exon and single exon genes to be used to test and train
gene-finding algorithms for Drosophila melanogaster genomic DNA.

UC Berkeley and LBNL provide these data sets "as is" in an effort to
create a common data set to be used by all gene-finding algorithms.
We encourage others to compare their results using these data sets.

Accompanying the data set is a ".sets" file listing 5 test/train
subsets.  These subsets can be used for cross-validation.


The files in this directory are:

	multi_exon_GB.dat.gz		GenBank format file 275 unique multi exon genes (less than 80% BLASTN identity between genes)
	multi_exon_GB.sets		proposed cross-validation sets

For specific training we have also split the complete Genbank entries 
into various gene feature sets:

	./CDS_v109/			complete CDS
	./intron_v109/			complete introns
	./exon_v109/			complete exons
	./promoter/			promoter sequences from the Eukaryotic Promoter Database (EPD) '98

	single_exon_GB.dat.gz		GenBank format file 141 single exon genes
	single_exon_GB.sets		proposed cross-validation sets


In addition to this highly curated gene set we extracted all possible
sequences in GenBank for Drosophila melanogaster that had CDS feature
annotation. For this set only genes with identical coding transcripts
were removed.

	multi_exon_GB_all.dat.gz	Additional GenBank format file 455 genes (only identical genes excluded) from mRNA and DNA entries in GenBank
	multi_exon_GB_all.sets		proposed cross-validation sets

For specific training we have also split the complete Genbank entries 
into various gene feature sets:

	./CDS_all_v109/			complete CDS
	./exon_all_v109/		complete exons
	./intron_all_v109/		complete introns

We also provide the Drosophila Genie data sets from 1996 and Spring 1998 in 
	./GENIE_96
and
	./GENIE_98

A highly curated coding transcript data set can be found in 
	ftp://www.fruitfly.org/seq_tools/datasets/OtherDataSets/ASHBURNER_97

In addition, several Perl and shell routines for generating
cross-validated sets are provided in the scripts directory
(http://www.fruitfly.org/seq_tools/datasets/scripts/).

=====
Martin Reese (LBNL) martinr@bdgp.lbl.gov
With help from:
David Kulp (UCSC) dkulp@cse.ucsc.edu
Andrew Gentles (Stanford)
Uwe Ohler (UCB) ohler@fruitfly.berkeley.edu