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Table 3 Detailed analysis of false positives of digIS, ISEScan, OASIS, and ISsaga on manually curated

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

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
  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.