Table 1.
Benchmarking of the ABFGP performance on validated genes compared to GeneMark-ES
| Species | 10 pooled species1 | Magnaporthe oryzae2 | Fusarium verticillioides | |||
|---|---|---|---|---|---|---|
| Method |
|
ABFGP |
ABFGP |
GeneMark-ES |
ABFGP |
GeneMark-ES |
| # unigenes |
|
6,965 |
956 |
169 |
1154 |
327 |
| Intron |
Sn |
91.16 |
91.5 |
89.3 |
92.2 |
90.7 |
| |
Pr |
97.08 |
97.4 |
90.5 |
98.2 |
94.3 |
| Exon |
Sn |
88.54 |
89.1 |
88.0 |
90.4 |
85.4 |
| |
Pr |
98.91 |
99.4 |
89.1 |
98.9 |
87.9 |
| Nucleotide |
Sn |
98.75 |
98.3 |
98.2 |
99.3 |
98.8 |
| |
Pr |
99.08 |
99.3 |
97.1 |
99.0 |
97.1 |
| Gene3 | Sn | 79.4 (5,533) | 81.7 (781) | n.a. | 82.1 (947) | n.a. |
Sensitivity (Sn) and precision (Pr) of the gene model components (introns, exons, nucleotides) are expressed in percentages. Sn is calculated as true positives divided by: (true positives + false negatives); and Pr as true positives divide by: (true positives + false positives) [3].
1A list of all ten fungal species and results per species are provided in Additional file 4.
2Formerly named Magnaporthe grisea.
3The gene sensitivity is the percentage of gene models that is predicted without a single error. Total number of correctly predicted gene models is indicated in between brackets. Gene sensitivity was not provided for GeneMark-ES.