Drosophila species gene prediction statistics
27 October 2005*

Genscan
ucsc

Species	euGenes matches	Dupl. genes	UCSC matches	Geneid ucsc	Snap han	Geneid han	Orth+Nor. venky	Ortholog venky
Dmel	13472	935	13449	16434	14147
Dsim	13246	1231	13024	16373	15151	14515	11439	13077	11368
Dyak	13043	1276	13279	20752	17621	17961	14463	13257	10701
Dere	13328	1141	13362	17531	0	0	0	13198	10211
Dana	13074	1528	13098	29704	0	0	0	12881	10484
Dpse	12858	1815	12834	16906	14883	17801	12266	12553	10379	Note 1
Dmoj	12675	1946	12675	21516	0	19360	17324	12238	8425
Dvir	12709	1389	12731	21080	0	17297	14792	12314	9658
Dgri	12615	2502	12635	23037	0	0	0	0	0
Notes
assemblies	2005			2005		2004		2004		Note 2

NOTE *: these are not using same genome assemblies. Differences among methods can be due to this along with other factors.
Results are a moving target, these numbers will change.

Columns:
Gene matches: tBLASTn for Dmel x other, Dmel prot. gene count and matches to that.
Dupl. genes: gene matches to >1 location.
Orth+Nor.venky = n genes in both ortholog and non-ortholog classes (all dmel matches)
Genscan.ucsc, Geneid.ucsc = predictions from UCSC
SNAP.han,Geneid.han = predictions from Berkeley Comparative Genomics group

Note 1: Dpse Twinscan.ucsc =18330 ; Genewise.ucsc = 18179

Note 2: Dgri.UCSC = 2005.08.01, Dgri.Gene matchs = 2005.08.31 assemblies, other 2005 assemblies are latest as of 2005.08.31

Note 3. Sources, latest assembly used
eugenes: ftp://eugenes.org/eugenes/genomes/
ucsc: http://hgdownload.cse.ucsc.edu/goldenPath/
han: http://hanuman.math.berkeley.edu/genomes/drosophila.html
venky: http://rana.lbl.gov/~venky/annotation/gff/

Don Gilbert, 28 Oct 2005

Developed at the Genome Informatics Lab of Indiana University Biology Department

Drosophila species gene prediction statistics 27 October 2005*

Drosophila species gene prediction statistics
27 October 2005*