Table 2 Performance evaluation of different tools to predict prophage locations (start/end sites)
Experimental data | Prediction | Evaluation | |||||
|---|---|---|---|---|---|---|---|
Prophage (range/length—including att sites) | Tool | Deviation from | Length | Precision | Recall | F-score | |
Start | End | ||||||
S. Tm LT2p22 p22 (1213987-1255756/41770) | PHASTER | 60 | 1126 | 42836 | 0.97 | 1.00 | 0.99 |
Prophage Hunter | −13077 | 8273 | 63120 | 0.66 | 1.00 | 0.80 | |
VIBRANT | 60 | −334 | 41376 | 1.00 | 0.99 | 1.00 | |
Virsorter | 10 | 1152 | 42912 | 0.97 | 1.00 | 0.99 | |
S. Tm LT2p22 Fels-1 (1849458-1892188/42731) | PHASTER | −1528 | −3284 | 40975 | 0.96 | 0.92 | 0.94 |
Prophage Hunter | −4528 | 7083 | 54342 | 0.79 | 1.00 | 0.88 | |
VIBRANT | 41 | 1216 | 43906 | 0.97 | 1.00 | 0.99 | |
Virsorter | −20661 | 22091 | 85483 | 0.50 | 1.00 | 0.67 | |
S. Tm LT2p22 Fels-2 (3731215-3764954/33740) | PHASTER | 0 | 1410 | 35150 | 0.96 | 1.00 | 0.98 |
Prophage Hunter | NA | NA | NA | NA | NA | NA | |
VIBRANT | 449 | 10659 | 43950 | 0.76 | 0.99 | 0.86 | |
Virsorter | −115370 | 79199 | 228309 | 0.15 | 1.00 | 0.26 | |
YL44 phage 1 (969482-1008291/38810) | PHASTER | NA | NA | NA | NA | NA | NA |
Prophage Hunter | −9199 | −2567 | 45442 | 0.80 | 0.93 | 0.86 | |
Prophage Hunter | 23847 | 3354 | 18317 | 0.82 | 0.39 | 0.52 | |
VIBRANT | 186 | −9968 | 28656 | 1.00 | 0.74 | 0.85 | |
Virsorter | 1436 | 138 | 37512 | 1.00 | 0.96 | 0.98 | |
Virsorter | 8087 | 138 | 30861 | 1.00 | 0.79 | 0.88 | |
YL44 phage 2 (2566025-2602918/36894) | PHASTER | NA | NA | NA | NA | NA | NA |
Prophage Hunter | −4041 | −23277 | 17658 | 0.77 | 0.37 | 0.50 | |
Prophage Hunter | 704 | −2995 | 33195 | 1.00 | 0.90 | 0.95 | |
Prophage Hunter | 7638 | 10625 | 39881 | 0.73 | 0.79 | 0.76 | |
VIBRANT | −10070 | −3356 | 43608 | 0.77 | 0.91 | 0.83 | |
Virsorter | −25233 | 44693 | 106820 | 0.35 | 1.00 | 0.51 | |
YL58 phage 1 (128601-174693/46093) | PHASTER | NA | NA | NA | NA | NA | NA |
Prophage Hunter | −2929 | −27047 | 21975 | 0.87 | 0.41 | 0.56 | |
Prophage Hunter | 139 | −49 | 45905 | 1.00 | 1.00 | 1.00 | |
VIBRANT | 153 | 3341 | 49281 | 0.93 | 1.00 | 0.96 | |
Virsorter | −1242 | 33898 | 81233 | 0.57 | 1.00 | 0.72 | |
E. coli HSÂ phage 1 (916812-948289/31478) | PHASTER | 78 | 3104 | 34504 | 0.91 | 1.00 | 0.95 |
Prophage Hunter | NA | NA | NA | NA | NA | NA | |
VIBRANT | 461 | 4880 | 35897 | 0.86 | 0.99 | 0.92 | |
Virsorter | 2787 | −41 | 28650 | 1.00 | 0.91 | 0.95 | |
YL31 phage 1 (1009760-1046747/36988) | PHASTER | −6510 | −17 | 43481 | 0.85 | 1.00 | 0.92 |
Prophage Hunter | −8493 | −9478 | 36003 | 0.76 | 0.74 | 0.75 | |
VIBRANT | −13474 | −185 | 50277 | 0.73 | 0.99 | 0.84 | |
Virsorter | −43160 | 4955 | 85103 | 0.43 | 1.00 | 0.61 | |
YL31 phage 2 (2984604-3026727/42124) | PHASTER | NA | NA | NA | NA | NA | NA |
Prophage Hunter | 0 | 0 | 42124 | 1.00 | 1.00 | 1.00 | |
Prophage Hunter | 10596 | 4114 | 35642 | 0.88 | 0.75 | 0.81 | |
VIBRANT | −828 | −914 | 42038 | 0.98 | 0.98 | 0.98 | |
Virsorter | −1257 | 983 | 44364 | 0.95 | 1.00 | 0.97 | |
KB18 phage 1 (2602856-2642096/39241) | PHASTER | −5132 | 7663 | 52036 | 0.75 | 1.00 | 0.86 |
Prophage Hunter | 3156 | 15738 | 51823 | 0.70 | 0.92 | 0.79 | |
VIBRANT | NA | NA | NA | NA | NA | NA | |
Virsorter | −45270 | 5505 | 90016 | 0.44 | 1.00 | 0.61 | |