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Table 2 Mean and standard deviation for gene prediction performance of our method (Neural Net) and MetaGene. Performance was measured on 700 bp fragments that were randomly excised from each test genome to 5-fold coverage (ten replications per species). The harmonic mean is a measure that combines sensitivity and specificity.

From: Gene prediction in metagenomic fragments: A large scale machine learning approach

  SENSITIVITY SPECIFICITY HARMONIC MEAN
Species Neural Net MetaGene Neural Net MetaGene Neural Net MetaGene
Archaeoglobus fulgidus 87.2 ± 0.21 93.7 ± 0.15 93.4 ± 0.16 92.7 ± 0.16 90.2 ± 0.17 93.2 ± 0.14
Methanococcus jannaschii 91.7 ± 0.17 95.8 ± 0.14 96.2 ± 0.13 92.7 ± 0.19 93.9 ± 0.10 94.3 ± 0.15
Natronomonas pharaonis 87.9 ± 0.22 95.1 ± 0.09 93.9 ± 0.10 92.7 ± 0.17 90.8 ± 0.16 93.9 ± 0.12
Buchnera aphidicola 90.6 ± 0.37 96.7 ± 0.24 95.3 ± 0.31 91.1 ± 0.29 92.9 ± 0.28 93.8 ± 0.21
Burkholderia pseudomallei 87.9 ± 0.11 94.1 ± 0.11 90.1 ± 0.09 85.1 ± 0.13 89.0± 0.08 89.4 ± 0.10
Bacillus subtilis 91.4 ± 0.16 89.8 ± 0.14 95.3 ± 0.09 89.3 ± 0.19 93.3 ± 0.10 89.5 ± 0.14
Corynebacterium jeikeium 89.7 ± 0.24 91.9 ± 0.12 93.8 ± 0.19 89.2 ± 0.21 91.7 ± 0.19 90.5 ± 0.13
Chlorobium tepidum 82.1 ± 0.25 85.7 ± 0.27 91.2 ± 0.17 88.4 ± 0.26 86.4 ± 0.19 87.0 ± 0.22
Escherichia coli 91.7 ± 0.16 93.3 ± 0.07 95.3 ± 0.09 90.9 ± 0.10 93.5 ± 0.12 92.1 ± 0.07
Helicobacter pylori 92.1 ± 0.11 90.2 ± 0.14 96.6 ± 0.15 89.6 ± 0.23 94.3 ± 0.11 89.9 ± 0.15
Pseudomonas aeruginosa 90.4 ± 0.14 96.2 ± 0.07 92.5 ± 0.11 91.4 ± 0.09 91.4 ± 0.12 93.7 ± 0.07
Prochlorococcus marinus 87.2 ± 0.21 93.7 ± 0.25 95.9 ± 0.14 90.8 ± 0.20 91.4 ± 0.15 92.2 ± 0.19
Wolbachia endosymbiont 87.2 ± 0.27 90.6 ± 0.42 85.2 ± 0.44 71.2 ± 0.54 86.2 ± 0.29 79.7 ± 0.45