Table 3.
Detailed analysis of false positives of digIS, ISEScan, OASIS, and ISsaga on manually curated
| Tool | Common metrics | Detailed classification of mFPs | Modified metrics | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| TP | FP | mFP | eIS | pNov | nIS | teIS | pNovDR (%) | nISDR (%) | pNov/nIS | |
| Dataset ISbrowser (N = 1192) | ||||||||||
| OASIS | 791 | 77 | 75 | 59 | 6 | 10 | 850 | 0.69 | 1.15 | 0.60 |
| ISEScan | 925 | 94 | 94 | 69 | 3 | 22 | 993 | 0.29 | 2.16 | 0.14 |
| ISEScan-fragments | 1077 | 248 | 239 | 103 | 18 | 118 | 1179 | 1.37 | 8.97 | 0.15 |
| ISsaga | 1135 | 363 | 323 | 148 | 31 | 144 | 1282 | 2.13 | 9.88 | 0.22 |
| digIS | 979 | 194 | 194 | 130 | 22 | 42 | 1108 | 1.88 | 3.58 | 0.52 |
| Dataset E. coli (N = 49) | ||||||||||
| OASIS | 26 | 4 | 4 | 4 | 0 | 0 | 30 | 0.00 | 0.00 | 0.00 |
| ISEScan | 43 | 8 | 7 | 3 | 0 | 4 | 46 | 0.00 | 8.00 | 0.00 |
| ISEScan-fragments | 45 | 18 | 17 | 6 | 0 | 11 | 51 | 0.00 | 17.74 | 0.00 |
| ISsaga | 48 | 29 | 28 | 10 | 0 | 18 | 58 | 0.00 | 23.68 | 0.00 |
| digIS | 43 | 11 | 11 | 6 | 0 | 5 | 49 | 0.00 | 9.26 | 0.00 |
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.