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Table 2 Performance of Spliceator and state-of-the-art programs on six independent benchmarks

From: Spliceator: multi-species splice site prediction using convolutional neural networks

  Accuracy Precision Sensitivity Specificity F1 Score
Donor Acceptor Donor Acceptor Donor Acceptor Donor Acceptor Donor Acceptor
Human           
 Spliceator 92.7 89.5 90.0 86.1 96.1 94.4 89.4 84.7 93.0 90.0
 SpliceFinder 91.5 91.1 76.9 73.3 97.0 99.8 89.6 88.2 85.8 84.5
 DSSP 93.2 91.0 96.9 94.4 89.2 87.1 97.2 94.8 92.9 90.6
 MaxEntScan 91.8 83.7 88.8 77.3 95.8 95.6 87.9 71.9 92.1 85.5
 NNSplice 68.4 65.9 62.3 61.5 89.2 86.7 48.5 44.8 73.4 72.0
Fish           
 Spliceator 95.0 91.3 91.6 86.0 99.0 98.7 90.9 84.0 95.1 91.9
 SpliceFinder 92.8 94.9 81.5 85.0 96.4 99.8 91.4 93.0 88.3 91.8
 DSSP 94.6 93.6 97.5 94.2 91.5 92.9 97.6 94.3 94.4 93.6
 MaxEntScan 93.9 83.3 90.6 75.4 98.1 99.0 89.8 67.7 94.2 85.6
 NNSplice 71.0 68.9 64.3 63.9 90.8 85.6 52.2 52.5 75.3 73.2
Fly           
 Spliceator 94.6 90.4 91.6 86.2 98.3 96.4 91.0 84.5 94.8 91.0
 SpliceFinder 92.1 90.9 79.8 72.8 95.8 99.8 90.7 88.0 87.1 84.2
 DSSP 94.0 91.6 96.6 93.1 91.3 89.8 96.7 93.4 93.9 91.4
 MaxEntScan 94.5 86.0 91.8 79.5 97.6 97.0 91.3 75.0 94.6 87.4
 NNSplice 71.7 71.1 65.3 64.8 91.4 92.1 52.3 50.3 76.2 76.1
Worm           
 Spliceator 93.9 88.8 91.4 86.9 96.9 91.4 90.9 86.2 94.1 89.1
 SpliceFinder 88.7 87.9 71.2 64.1 93.3 99.3 87.1 84.8 80.8 77.9
 DSSP 90.4 84.1 97.0 93.1 83.4 73.6 97.4 94.5 89.7 82.2
 MaxEntScan 92.9 82.0 91.6 76.8 94.5 92.0 91.3 72.1 93.0 83.7
 NNSplice 65.8 57.8 61.9 58.0 80.3 56.4 51.7 59.2 69.9 57.1
Plant           
 Spliceator 94.7 90.6 91.8 89.1 98.1 92.7 91.3 88.6 94.9 90.8
 SpliceFinder 88.9 87.6 72.2 63.1 92.9 99.3 87.5 84.4 81.3 77.2
 DSSP 88.2 85.1 96.5 94.2 79.3 74.8 97.1 95.4 87.1 83.3
 MaxEntScan 92.4 85.3 90.5 79.2 94.6 95.9 90.1 74.8 92.5 86.7
 NNSplice 59.8 59.2 57.2 57.1 78.4 71.3 41.0 47.3 66.2 63.4
PVP           
 Spliceator 86.0 83.5 82.9 83.1 90.8 84.0 81.2 82.9 86.6 83.6
 SpliceFinder 87.3 89.3 67.9 58.8 77.6 98.6 89.9 87.7 72.4 73.8
 DSSP 84.3 76.6 92.5 84.7 74.6 65.0 93.9 88.2 82.6 73.5
 MaxEntScan 84.5 80.0 81.0 75.4 90.1 89.4 79.1 70.4 85.2 81.8
 NNSplice 64.8 63.7 60.4 61.4 85.8 73.9 43.6 53.5 70.9 67.1
Average           
 Spliceator 92.82 89.02 89.88 86.23 96.53 92.93 89.12 85.15 93.08 89.40
 SpliceFinder 90.22 90.28 74.92 69.52 92.17 99.43 89.37 87.68 82.62 81.57
 DSSP 90.78 87.00 96.17 92.28 84.88 80.51 96.65 93.43 90.10 85.77
 MaxEntScan 91.67 83.38 89.05 77.27 95.12 94.82 88.25 71.98 91.93 85.12
 NNSplice 66.92 64.43 61.90 61.12 85.98 77.67 48.22 51.27 71.98 68.15
  1. Performance metrics for Spliceator, SpliceFinder, DSSP, MaxEntScan, and NNSplice, using six independent benchmarks from model and non-model organisms: human, fish, fly, worm, plant and PVP (Protists + Viridiplantae) (values in bold correspond to the highest performance)