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Table 1 Sensitivity, Specificity and F1 scores of transcripts generated by multiple gene annotation pipelines for three model organisms—Arabidopsis thaliana, Oryza sativa and Zea mays

From: FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

  Arabidopsis thaliana Oryza sativa Zea mays (NCBI)
BRAKER2 MAKER2 PASA FINDER FINDER + BRAKER2 FINDER + BRAKER2 + PROTEIN BRAKER2 MAKER2 PASA FINDER FINDER + BRAKER2 FINDER + BRAKER2 + PROTEIN BRAKER2 MAKER2 PASA FINDER FINDER + BRAKER2 FINDER + BRAKER2 + PROTEIN
Base specificity 91.08 74.87 62.71 74.46 75.01 75.04 57.63 52.67 36.77 42.46 42.6 42.75 6.52 45.22 60.39 62.97 62.96 62.92
Base sensitivity 60.27 52.55 69.41 71.45 74.14 74.23 36.85 40.17 59.19 61.43 61.83 62.37 50.43 54.38 66.7 72.1 72.15 72.16
Base F1 score 72.54 61.76 65.89 72.92 74.57 74.63 44.95 45.58 45.36 50.21 50.44 50.73 11.55 49.38 63.39 67.23 67.24 67.22
Exon specificity 80.28 95.35 90.74 91.79 91.43 91.43 38.4 72.31 67.37 67.67 67.5 67.62 15.96 65.14 84.26 79.71 79.59 79.57
Exon sensitivity 73.29 55.04 67.49 69.93 71.62 71.7 53.74 50.59 63.99 64.81 65.22 66.06 65.65 61.84 71.84 74.38 74.4 74.4
Exon F1 score 76.63 69.79 77.41 79.38 80.32 80.37 44.79 59.53 65.64 66.21 66.34 66.83 25.68 63.45 77.56 76.95 76.91 76.9
Intron specificity 86 98.26 95.98 96.55 96.26 96.26 52.8 76.87 72.36 73.24 73.19 73.26 21.77 74.41 88.45 84.86 84.78 84.76
Intron sensitivity 84.25 60.64 76.11 76.51 78.33 78.42 76.78 55.77 70.44 71.03 71.52 72.34 80.88 64.99 75.19 78.12 78.15 78.15
Intron F1 score 85.12 75 84.9 85.37 86.37 86.43 62.57 64.64 71.39 72.12 72.35 72.8 34.31 69.38 81.28 81.35 81.33 81.32
Transcript specificity 49.91 76.9 55.21 60.04 59.82 59.82 12.71 40.13 23.17 24.54 24.59 24.54 2.75 32.67 48.6 44.78 44.84 44.78
Transcript sensitivity 30.26 21.74 28.62 37.21 39.21 39.28 16.35 18.01 29.51 33 33.32 33.82 19.57 25.01 37.94 42.25 42.3 42.31
Transcript F1 score 37.68 33.9 37.7 45.95 47.37 47.42 14.3 24.86 25.96 28.15 28.3 28.44 4.82 28.33 42.61 43.48 43.53 43.51
Gene specificity 51.58 76.9 61.79 67.33 66.56 66.55 13.46 40.13 36.81 32.79 32.76 32.38 2.78 32.67 55.69 52.3 52.29 52.19
Gene sensitivity 50.43 37.2 44.39 57.96 61.3 61.4 18.07 19.4 31.37 35.05 35.4 35.96 29.02 38.14 51.57 57.35 57.42 57.43
Gene F1 score 51 50.14 51.66 62.29 63.82 63.87 15.43 26.16 33.87 33.88 34.03 34.08 5.07 35.19 53.55 54.71 54.74 54.68
  1. Best performance is indicated by bold values