Table 5 CDS assessment at the transcript and gene levels
From: EGASP: the human ENCODE Genome Annotation Assessment Project
| Â | Transcript | Gene | Â | ||
|---|---|---|---|---|---|
| Â | TSn | TSp | GSn | GSp | Ratio CDS/UTR |
Category 1 | Â | Â | Â | Â | Â |
   AUGUSTUS-any | 22.65% | 35.59% | 47.97% | 35.59% | 100.00% |
   FGENESH++ | 36.21% | 41.61% | 69.93% | 42.09% | 78.25% |
   JIGSAW | 34.05% | 65.95% | 72.64% | 65.95% | 100.00% |
   PAIRAGON-any | 39.29% | 60.34% | 69.59% | 61.32% | 62.92% |
Category 2 | Â | Â | Â | Â | Â |
   AUGUSTUS-abinit | 11.09% | 17.22% | 24.32% | 17.22% | 100.00% |
   GENEMARK.hmm-A | 6.93% | 3.24% | 15.20% | 3.24% | 100.00% |
   GENEMARK.hmm-B | 7.70% | 7.91% | 16.89% | 7.91% | 100.00% |
   GENEZILLA | 9.09% | 8.84% | 19.59% | 8.84% | 100.00% |
Category 3 | Â | Â | Â | Â | Â |
   ACEVIEW | 44.68% | 19.31% | 63.51% | 48.65% | 49.15% |
   AUGUSTUS-EST | 22.50% | 37.01% | 47.64% | 37.01% | 100.00% |
   ENSEMBL | 39.75% | 54.64% | 71.62% | 67.32% | 65.77% |
   EXOGEAN | 42.53% | 52.44% | 63.18% | 80.82% | 59.60% |
   EXONHUNTER | 10.48% | 6.33% | 21.96% | 6.33% | 100.00% |
   PAIRAGON+NSCAN_EST | 39.29% | 60.64% | 69.59% | 61.71% | 62.89% |
Category 4 | Â | Â | Â | Â | Â |
   AUGUSTUS-dual | 12.33% | 18.64% | 26.01% | 18.64% | 100.00% |
   DOGFISH | 5.08% | 14.61% | 10.81% | 14.61% | 100.00% |
   MARS | 15.87% | 15.11% | 33.45% | 24.94% | 100.00% |
   NSCAN | 16.95% | 36.71% | 35.47% | 36.71% | 79.80% |
   SAGA | 2.16% | 3.44% | 4.39% | 3.44% | 100.00% |
UCSC Tracks | Â | Â | Â | Â | Â |
   ACEMBLY | 33.90% | 7.96% | 54.39% | 21.24% | 48.56% |
   CCDSgene | 28.97% | 85.58% | 55.41% | 89.39% | 100.00% |
   ECgene | 56.86% | 8.84% | 79.05% | 12.42% | 46.11% |
   ENSgene | 40.52% | 54.09% | 73.99% | 68.30% | 65.62% |
   GENEID | 4.78% | 8.78% | 10.47% | 8.78% | 100.00% |
   GENSCAN | 7.40% | 10.13% | 15.54% | 10.13% | 100.00% |
   KNOWNgene | 43.45% | 46.93% | 77.03% | 72.79% | 60.03% |
   MGCgene | 23.73% | 78.24% | 49.32% | 82.56% | 63.43% |
   REFgene | 41.91% | 75.21% | 77.03% | 82.76% | 61.82% |
   SGPgene | 8.17% | 12.59% | 17.57% | 12.59% | 100.00% |
   TWINSCAN | 10.63% | 20.25% | 22.30% | 20.25% | 100.00% |