Table V. Comparison of PromPredict with EP3 (Abeel et al., 2008a).
In Arabidopsis, 20,094 (protein-coding) and 1,263 (RNA-coding) TSSs were considered for analysis. In rice, 23,057 (protein-coding) and 1,527 (RNA-coding) TSSs were considered for analysis. For Arabidopsis, PromPredict gave 386,264 predictions while EP3 gave 594,559 predictions. PromPredict predicted 1,284,547 signals and EP3 predicted 1,611,598 signals in the rice genome. The region considered for determining true positives is −500 to +500 bp of the TSS for protein-coding genes and −1,000 to 0 bp of the TSS for ncRNA genes.
| Feature | PromPredict |
EP3 |
||
| Protein | RNA | Protein | RNA | |
| Arabidopsis | ||||
| Recall | 0.96 | 0.94 | 0.48 | 0.28 |
| Precision | 0.42 | 0.75 | 0.49 | 0.51 |
| F value | 0.58 | 0.83 | 0.48 | 0.37 |
| TPpred. length (nucleotides)a | 71.6 ± 47.8 | 64.6 ± 45 | 400 | 400 |
| FPpred. length (nucleotides)a | 53.9 ± 38.9 | 61.6 ± 41.9 | 400 | 400 |
| TP coverage (%) | 13.9 | 12.7 | 50.7 | 46 |
| FP coverage (%) | 7.5 | 7.6 | 13.2 | 24.5 |
| Rice | ||||
| Recall | 0.97 | 0.95 | 0.77 | 0.15 |
| Precision | 0.31 | 0.9 | 0.62 | 0.86 |
| F value | 0.47 | 0.92 | 0.53 | 0.26 |
| TPpred. length (nucleotides)a | 94.6 ± 60.1 | 66.2 ± 48.8 | 400 | 400 |
| FPpred. length (nucleotides)a | 60.7 ± 44.5 | 45.8 ± 36.2 | 400 | 400 |
| TP coverage (%) | 17.9 | 14.2 | 51.8 | 7.6 |
| FP coverage (%) | 8.5 | 6 | 10.4 | 6.7 |
a
In PromPredict, the midpoint of a 100-nucleotide window is considered as a prediction if it satisfies the cutoffs. In EP3, the entire 400-nucleotide window is considered as a prediction if it satisfies the cutoffs.