Table 2.

Assessment of DNA structural features for their ability to differentiate between promoter and non-promoter sequences in six different model organisms

Organism	Number of sequences	First cycle			Second cycle			Property
		Prec.	BA	F-score	Prec.	BA	F-score
H. pylori	706	77	75	75	80	75	72	STB
Anabaena	2513	72	71	70	76	71	68
Synechocystis	1639	69	69	69	74	69	65
E. coli	1331	74	75	76	80	77	76
Salmonella	981	75	76	77	79	77	76
Klebsiella	1324	80	80	80	84	81	80
H. pylori	706	54	56	63	56	58	63	BDC
Anabaena	2513	52	54	62	53	53	58
Synechocystis	1639	52	53	61	53	53	57
E. coli	1331	54	56	63	55	57	61
Salmonella	981	55	57	65	56	58	62
Klebsiella	1324	56	59	66	59	61	65
H. pylori	706	54	54	55	58	56	51	BNC
Anabaena	2513	55	57	64	57	58	61
Synechocystis	1639	52	53	62	53	54	59
E. coli	1331	52	54	63	52	53	59
Salmonella	981	52	53	62	52	53	59
Klebsiella	1324	51	52	63	51	51	59
H. pylori	706	53	55	62	54	55	59	CBC
Anabaena	2513	53	54	60	55	55	58
Synechocystis	1639	53	54	61	53	54	58
E. coli	1331	57	58	63	58	59	60
Salmonella	981	56	58	64	59	60	63
Klebsiella	1324	58	60	66	59	60	64

Out of the total test dataset (promoters associated with the primary category of TSS), 1001 nucleotide long sequences with 30–65% GC content were considered. The sequences with promoter predictions falling in the 300 nucleotide region spanning −200 to +100 with respect to TSS at 0 were considered as TP while sequences with predictions falling in the coding region +200 to + 500 with respect to TSS were labelled as FP. Evaluation parameters precision (Prec.), BA and F-score were calculated using formulas explained in the ‘Material and methods’ section.