Table 1 Benchmark results on the BRAKER1 test sets
From: Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
MAKER2 + (exonerate) | GeMoMa + without RNA-seq data | GeMoMa + with RNA-seq data | RNAseq-Cufflinks | RNAseq-StringTie | BRAKER1 ∗ | MAKER2 ∗ | CodingQuarry ∗ | MAKER2 + (exonerate, Trinity, Augustus) | MAKER2 + (GeMoMa, Trinity, Augustus) | |
|---|---|---|---|---|---|---|---|---|---|---|
Arabidopsis thaliana | ||||||||||
(ref. A. lyrata) | ||||||||||
Gene Sn | 44.0 | 61.3 | 66.5 | 28.9 | 35.9 | 64.4 | 51.3 | NA | 56.9 | 57.9 |
Gene Sp | 47.8 | 65.7 | 71.3 | 47.9 | 59.1 | 52.0 | 52.5 | NA | 65.7 | 67.8 |
Transcript Sn | 37.5 | 52.2 | 57.2 | 26.6 | 33.7 | 55.0 | 43.5 | NA | 48.3 | 49.1 |
Transcript Sp | 47.8 | 65.7 | 65.3 | 35.6 | 48.3 | 50.9 | 52.5 | NA | 65.7 | 67.8 |
Exon Sn | 70.0 | 79.3 | 80.6 | 58.1 | 60.8 | 82.9 | 76.1 | NA | 81.8 | 82.1 |
Exon Sp | 81.9 | 86.6 | 87.5 | 81.9 | 87.1 | 79.0 | 76.1 | NA | 87.5 | 88.6 |
Caenorhabditis elegans | ||||||||||
(ref. C. briggsae) | ||||||||||
Gene Sn | 26.2 | 39.6 | 49.1 | 18.7 | 22.6 | 55.0 | 41.0 | NA | 40.5 | 47.3 |
Gene Sp | 38.0 | 49.9 | 63.8 | 29.1 | 36.1 | 55.2 | 30.8 | NA | 51.5 | 56.4 |
Transcript Sn | 21.0 | 30.7 | 39.8 | 16.2 | 20.0 | 43.0 | 31.3 | NA | 31.4 | 36.2 |
Transcript Sp | 38.0 | 49.9 | 58.7 | 24.1 | 30.1 | 53.2 | 30.8 | NA | 51.5 | 56.4 |
Exon Sn | 50.3 | 64.2 | 67.1 | 54.4 | 59.1 | 80.2 | 69.4 | NA | 70.5 | 75.2 |
Exon Sp | 82.6 | 81.5 | 87.5 | 81.3 | 84.1 | 85.3 | 62.3 | NA | 85.6 | 86.7 |
Drosophila melanogaster | ||||||||||
(ref. D. simulans) | ||||||||||
Gene Sn | 64.3 | 78.2 | 83.1 | 55.7 | 55.2 | 64.9 | 55.2 | NA | 61.5 | 64.0 |
Gene Sp | 69.2 | 81.6 | 87.1 | 71.3 | 73.5 | 59.4 | 46.3 | NA | 69.6 | 71.9 |
Transcript Sn | 44.1 | 52.9 | 65.0 | 48.7 | 49.0 | 46.1 | 38.5 | NA | 42.7 | 44.3 |
Transcript Sp | 69.2 | 81.6 | 81.2 | 60.1 | 65.7 | 57.9 | 46.3 | NA | 69.6 | 71.9 |
Exon Sn | 69.0 | 76.3 | 80.0 | 67.8 | 66.2 | 75.0 | 66.5 | NA | 74.3 | 76.3 |
Exon Sp | 89.1 | 92.0 | 93.3 | 85.4 | 88.3 | 81.7 | 66.9 | NA | 88.0 | 89.1 |
Schizosaccharomyces pombe | ||||||||||
(ref. S. octosporus) | ||||||||||
Gene Sn | 49.2 | 76.4 | 79.2 | 69.0 | 65.8 | 77.4 | 42.8 | 79.7 | 71.6 | 74.6 |
Gene Sp | 59.9 | 84.6 | 88.0 | 93.8 | 92.5 | 80.5 | 68.7 | 72.6 | 88.1 | 89.1 |
Transcript Sn | 49.2 | 76.4 | 79.2 | 69.0 | 65.8 | 77.4 | 42.8 | 79.7 | 71.6 | 74.6 |
Transcript Sp | 59.9 | 84.6 | 87.6 | 80.5 | 71.3 | 76.5 | 68.7 | 72.6 | 88.1 | 89.1 |
Exon Sn | 56.1 | 81.6 | 83.1 | 77.2 | 77.7 | 83.2 | 50.1 | 79.6 | 79.2 | 81.2 |
Exon Sp | 73.3 | 88.6 | 91.9 | 87.6 | 81.7 | 83.2 | 71.4 | 81.7 | 92.0 | 92.6 |