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

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

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
  1. 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.