Table 4.
Performance of digIS against ISEScan, OASIS, and ISsaga on NCBI GenBank datasets
| Tool | N | Detailed classification of mFPs | Modified metrics | |||||
|---|---|---|---|---|---|---|---|---|
| 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.