Table 1 F1-score on CDS, transcript, and gene level for BRAKER1 (RNA-seq hints), BRAKER2 (protein hints of type (iii)), TSEBRA_EVM, EVM using comparable evidence, and TSEBRA (default hyperparameter) with hints generated by the BRAKER runs
CDS level F1-score | |||||
|---|---|---|---|---|---|
BRAKER1 | BRAKER2 | EVM | TSEBRA _EVM | TSEBRA | |
A. tha. | 81.87 | 84.01 | 84.41 | 86.21 | 86.90 |
B. ter. | 76.12 | 72.84 | 77.80 | ||
C. ele. | 85.87 | 81.13 | 86.14 | 85.13 | 84.48 |
D. mel. | 79.82 | 76.79 | 79.67 | 79.89 | 81.66 |
D. rer. | 74.00 | 72.23 | 78.40 | ||
M. tru. | 71.46 | 75.11 | 80.98 | ||
P. tep. | 68.61 | 63.90 | 67.96 | ||
P. tri. | 78.32 | 83.40 | 87.60 | ||
R. pro. | 53.54 | 54.49 | 56.30 | ||
T. nig. | 53.95 | 57.97 | 58.70 | ||
X. tro. | 74.96 | 75.89 | 79.44 | ||
Transcript level F1-score | |||||
|---|---|---|---|---|---|
BRAKER1 | BRAKER2 | EVM | TSEBRA_EVM | TSEBRA | |
A. tha. | 53.78 | 56.63 | 57.32 | 61.35 | 62.00 |
B. ter. | 33.15 | 26.49 | 35.02 | ||
C. ele. | 53.30 | 42.71 | 52.76 | 54.46 | 55.94 |
D. mel. | 51.33 | 46.94 | 49.90 | 53.76 | 55.18 |
D. rer. | 24.99 | 22.17 | 33.43 | ||
M. tru. | 39.04 | 44.09 | 51.72 | ||
P. tep. | 26.14 | 18.04 | 28.89 | ||
P. tri. | 47.04 | 55.96 | 62.31 | ||
R. pro. | 12.84 | 12.65 | 15.22 | ||
T. nig. | 5.74 | 7.93 | 9.78 | ||
X. tro. | 22.88 | 23.84 | 31.83 | ||
Gene level F1-score | |||||
|---|---|---|---|---|---|
BRAKER1 | BRAKER2 | EVM | TSEBRA_EVM | TSEBRA | |
A. tha. | 65.51 | 70.58 | 70.88 | 78.35 | 79.69 |
B. ter. | 38.91 | 32.18 | 44.71 | ||
C. ele. | 63.13 | 52.29 | 63.98 | 68.90 | 70.78 |
D. mel. | 64.44 | 61.25 | 64.94 | 71.34 | 73.93 |
D. rer. | 31.49 | 27.37 | 44.13 | ||
M. tru. | 40.03 | 44.96 | 54.05 | ||
P. tep. | 28.59 | 19.99 | 33.83 | ||
P. tri. | 53.11 | 63.88 | 73.45 | ||
R. pro. | 13.64 | 12.91 | 16.21 | ||
T. nig. | 6.59 | 8.87 | 11.46 | ||
X. tro. | 26.40 | 30.58 | 41.26 | ||