Table 4.

Glimmer3 prediction accuracy compared to other gene-finding systems

Genome		versus GeneMark.hmm			versus EasyGene 1.2			versus GeneMarkS
Organism	# Genes	3′ Match	5′ & 3′	Extra	3′ Match	5′ & 3′	Extra	3′ Match	5′ & 3′	Extra
A.fulgidus	1165	+4	−20	−86	+5	−25	+119	0	+2	−71
B.anthracis	3132	−2	−48	−134	+13	−63	+175	+1	+412	−142
B.subtilis	1576	+2	+280	+87	+15	−10	+536	−5	−39	+193
C.tepidum	1292	+1	+21	+19	+10	+9	+182	+1	−14	+29
C.perfringens	1504	−2	+177	−120	−2	−8	−21	−3	−14	−139
E.coli	3603	−25	+18	+188	+60	+44	+407	−25	−29	+190
G.sulfurreducens	2351	+13	+215	+34	+5	−1	+60	+14	+41	+66
H.pylori	915	−1	−3	−55	+4	−6	+148	−1	−8	−41
P.fluorescens	4535	+17	+288	+59	NA	NA	NA	+17	+479	+46
R.solanacearum	2512	+7	+183	+225	+11	+48	+193	−3	+160	+190
S.epidermidis	1650	+3	−32	−40	NA	NA	NA	+6	+204	−64
T.pallidum	575	+2	−8	+94	+8	−8	+176	−2	−18	+90
Averages:		+2	+89	+23	+13	−2	+198	+2	+98	+29

Glimmer3 predictions are as in the preceding table and each entry is the Glimmer3 value minus the corresponding value for the other gene-finder. GeneMark.hmm results were taken from the GeneMarkHMM files downloaded from NCBI. EasyGene 1.2 results were downloaded from http://servers.binf.ku.dk/cgi-bin/easygene.search GeneMarkS results were obtained from the server at http://exon.gatech.edu/GeneMark/genemarks.cgi None of these systems had results for Ureaplasma parvum, which uses a non-standard translation code. NA entries indicate strains that were not available for download.