PanDelos: a dictionary-based method for pan-genome content discovery

BMC Bioinformatics

Table 7 Performances of PanDelos, EDGAR and Roary on the synthetic datasets

			TP	FP	FN	TN	f-measure	CDiff
PanDelos
G37	0.5%	Roots	1,263,632	0	2324	1,386,060,388	0.9991	1
M129	0.5%	Roots	1,689,082	0	4060	2,460,563,516	0.9988	2
G37	1%	Roots	1,259,344	0	5310	1,385,219,936	0.9979	0
M129	1%	Roots	1,689,682	0	3024	2,467,589,288	0.9991	0
G37	0.5%	Leaves	1,278,188	0	25,374	1,756,053,000	0.9902	24
M129	0.5%	Leaves	1,695,228	0	47,376	3,086,359,452	0.9862	57
G37	1%	Leaves	1,270,658	0	45,042	1,735,332,524	0.9826	64
M129	1%	Leaves	1,773,110	196	57,320	3,144,153,456	0.9840	210
EDGAR
G37	0.5%	Roots	1,258,382	0	7574	1,386,060,388	0.9970	34
M129	0.5%	Roots	1,663,846	0	29,296	2,460,563,516	0.9913	139
G37	1%	Roots	1,253,564	0	11,090	1,385,219,936	0.9956	48
M129	1%	Roots	1,665,186	0	27,520	2,467,589,288	0.9918	132
G37	0.5%	Leaves	1,269,670	0	33,892	1,756,053,000	0.9868	154
M129	0.5%	Leaves	1,671,400	0	71,204	3,086,359,452	0.9791	319
G37	1%	Leaves	1,269,724	0	45,976	1,735,332,524	0.9822	197
M129	1%	Leaves	1,753,318	98	77,112	3,144,153,554	0.9785	267
Roary
G37	0.5%	Roots	1,212,344	0	53,612	1,386,060,388	0.9784	179
M129	0.5%	Roots	1,598,840	856	94,302	2,460,562,660	0.9711	247
G37	1%	Roots	1,166,946	0	97,708	1,385,219,936	0.9598	383
M129	1%	Roots	1,541,422	1244	151,284	2,467,588,044	0.9529	537
G37	0.5%	Leaves	348,356	112	955,206	1,756,052,888	0.4217	3520
M129	0.5%	Leaves	423,836	154	1,318,768	3,086,359,298	0.3912	5619
G37	1%	Leaves	97,710	24	1,217,990	1,735,332,500	0.1383	6302
M129	1%	Leaves	468,466	64	1,361,964	3,144,153,588	0.4075	4674

ISSN: 1471-2105