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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
  1. The target species are given in multi-column rows. The same reference species, which is given in brackets, is used for all tools using homology-based gene prediction indicated by plus. The asterisks indicates that the performance of BRAKER1, MAKER2 and CodingQuarry is given as reported in [11]. The highest value per line is depicted in bold-face