Table 4 CDS assessment: summary of accuracy measures for CDS features at the nucleotide and exon levels
From: EGASP: the human ENCODE Genome Annotation Assessment Project
| Â | Nucleotide | Exon | |||||
|---|---|---|---|---|---|---|---|
| Â | NSn | NSp | N CC | ESn | ESp | ME | WE |
Category 1 | Â | Â | Â | Â | Â | Â | Â |
   AUGUSTUS-any | 94.42% | 82.43% | 0.88 | 74.67% | 76.76% | 8.25% | 16.29% |
   FGENESH++ | 91.09% | 76.89% | 0.83 | 75.18% | 69.31% | 9.73% | 24.64% |
   JIGSAW | 94.56% | 92.19% | 0.93 | 80.61% | 89.33% | 6.22% | 7.78% |
   PAIRAGON-any | 87.77% | 92.78% | 0.90 | 76.85% | 88.91% | 11.18% | 6.82% |
Category 2 | Â | Â | Â | Â | Â | Â | Â |
   AUGUSTUS-abinit | 78.65% | 75.29% | 0.76 | 52.39% | 62.93% | 29.09% | 24.82% |
   GENEMARK.hmm-A | 78.43% | 37.97% | 0.53 | 50.58% | 29.01% | 27.86% | 63.27% |
   GENEMARK.hmm-B | 76.09% | 62.94% | 0.69 | 48.15% | 47.25% | 31.77% | 40.68% |
   GENEZILLA | 87.56% | 50.93% | 0.66 | 62.08% | 50.25% | 19.14% | 41.93% |
Category 3 | Â | Â | Â | Â | Â | Â | Â |
   ACEVIEW | 90.94% | 79.14% | 0.84 | 85.75% | 56.98% | 4.38% | 16.69% |
   AUGUSTUS-EST | 92.62% | 83.45% | 0.88 | 74.10% | 77.40% | 9.01% | 15.61% |
   ENSEMBL | 90.18% | 92.02% | 0.91 | 77.53% | 82.65% | 9.99% | 9.22% |
   EXOGEAN | 84.18% | 94.33% | 0.89 | 79.34% | 83.45% | 9.88% | 5.06% |
   EXONHUNTER | 90.46% | 59.67% | 0.73 | 64.44% | 41.77% | 14.29% | 50.94% |
   PAIRAGON+NSCAN_EST | 87.56% | 92.77% | 0.90 | 76.63% | 88.95% | 11.51% | 6.85% |
Category 4 | Â | Â | Â | Â | Â | Â | Â |
   AUGUSTUS-dual | 88.86% | 80.15% | 0.84 | 63.06% | 69.14% | 16.82% | 19.60% |
   DOGFISH | 64.81% | 88.24% | 0.74 | 53.11% | 77.34% | 32.67% | 11.70% |
   MARS | 84.25% | 74.13% | 0.78 | 65.56% | 61.65% | 20.26% | 26.10% |
   NSCAN | 85.38% | 89.02% | 0.87 | 67.66% | 82.05% | 17.11% | 10.93% |
   SAGA | 52.54% | 81.39% | 0.65 | 38.82% | 50.73% | 40.48% | 27.85% |
UCSC Tracks | Â | Â | Â | Â | Â | Â | Â |
   ACEMBLY | 96.43% | 58.47% | 0.74 | 84.66% | 38.32% | 2.71% | 28.55% |
   CCDSgene | 56.87% | 99.52% | 0.75 | 51.95% | 97.75% | 40.38% | 0.27% |
   ECgene | 96.36% | 47.30% | 0.66 | 86.22% | 35.08% | 2.64% | 45.92% |
   ENSgene | 91.39% | 91.92% | 0.92 | 77.71% | 82.39% | 9.80% | 9.21% |
   GENEID | 76.77% | 76.48% | 0.76 | 53.84% | 61.08% | 27.86% | 27.26% |
   GENSCAN | 84.17% | 60.60% | 0.71 | 58.65% | 46.37% | 19.50% | 42.91% |
   KNOWNgene | 89.10% | 93.61% | 0.91 | 78.11% | 82.28% | 10.27% | 4.30% |
   MGCgene | 44.06% | 97.56% | 0.65 | 42.95% | 93.61% | 49.28% | 2.68% |
   REFgene | 85.34% | 98.50% | 0.92 | 73.23% | 94.67% | 15.38% | 1.22% |
   SGPgene | 82.81% | 82.20% | 0.82 | 60.56% | 65.16% | 19.36% | 22.85% |
   TWINSCAN | 78.16% | 84.59% | 0.81 | 58.43% | 73.11% | 24.64% | 16.30% |