digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes

BMC Bioinformatics

Table 4 Performance of digIS against ISEScan, OASIS, and ISsaga on NCBI GenBank datasets

Tool	N	Detailed classification of mFPs				Modified metrics
Tool	N	mFP	eIS	pNov	nIS	pNovDR (%)	nISDR (%)	pNov/nIS
Dataset ISbrowser (N = 1192)
OASIS	895	852	828	10	14	1.17	1.64	0.71
ISEScan	1006	993	954	9	30	0.91	3.02	0.30
ISEScan-fragments	1326	1283	1089	41	153	3.20	11.93	0.27
ISsaga	1786	1459	1188	75	196	5.14	13.43	0.38
digIS	1170	1157	1051	50	56	4.32	4.84	0.89
Dataset NCBI Archaea (341 genomes)
OASIS	5885	5789	5382	100	307	1.73	5.30	0.33
ISEScan	8404	8266	7532	207	527	2.50	6.38	0.39
ISEScan-fragments	12,016	11,550	9622	472	1456	4.09	12.61	0.32
ISsaga	17,698	14,788	10,946	822	3020	5.56	20.42	0.27
digIS	10,607	10,548	8640	728	1180	6.90	11.19	0.62
Dataset NCBI Bacteria (random selection of 2475 genomes)
OASIS	88,552	87,428	83,992	1176	2260	1.35	2.58	0.52
ISEScan	111,974	110,357	102,266	3274	4817	2.97	4.36	0.58
ISEScan-fragments	151,540	145,248	119,392	6096	19760	4.20	13.60	0.31
ISsaga	217,345	181,880	136,903	8479	36,498	4.66	20.07	0.23
digIS	134,851	132,877	118,805	6722	7350	5.06	5.53	0.91

N represents the number of outputs found by the tool; mFP represents the number of False Positives after merging fragments or ORFs referencing the same IS element; eIS, pNov, and nIS represent the number of mFPs classified into categories IS element with a high level of evidence, Distant or putative novel IS element, and Improbable or not an IS element, respectively; pNovDR is putative Novel Discovery Rate; nISDR is Improbable or not an IS element Discovery Rate, and pNov/nIS shows the ratio between the number of putative novel IS elements and improbable or not an IS elements.

ISSN: 1471-2105