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Table 4 Comparison of specificity, sensitivity and F1 scores of transcripts assemblies generated by Strawberry, Scallop, Stringtie, PsiCLASS and FINDER for three model organisms—A. thaliana, O. sativa and Z. 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 (RefSeq)
STRAWBERRY SCALLOP STRINGTIE PSICLASS FINDER STRAWBERRY SCALLOP STRINGTIE PSICLASS FINDER STRAWBERRY SCALLOP STRINGTIE PSICLASS FINDER
Base specificity 38.41 37.34 58.35 62.63 74.46 22.6 24.23 39.83 36.64 42.46 30.06 29.6 49.33 55.61 62.97
Base sensitivity 87.06 85.3 80.22 70.83 71.45 78.2 77.64 70.87 60.27 61.43 81.2 79.08 76.98 70.52 72.1
Base F1 score 53.3 51.94 67.56 66.48 72.92 35.07 36.93 51 45.57 50.21 43.88 43.08 60.13 62.18 67.23
Exon specificity 43.86 70.64 74.82 89.82 91.79 23.51 42.97 51.7 66.29 67.67 37.18 52.37 60.33 77.76 79.71
Exon sensitivity 85.3 79.67 79.29 69.54 69.93 79.08 76.65 75.47 65.75 64.81 85.03 81.68 81.77 75.88 74.38
Exon F1 score 57.93 74.88 76.99 78.39 79.38 36.24 55.07 61.36 66.02 66.21 51.74 63.82 69.43 76.81 76.95
Intron specificity 55.32 78.7 80.58 95.29 96.55 29.13 48.56 56.5 71.41 73.24 43.79 56.74 64.79 82.8 84.86
Intron sensitivity 92.06 89.99 87.75 77.63 76.51 85.84 85.41 83.28 71.72 71.03 90.19 86.69 86.05 78.99 78.12
Intron F1 score 69.11 83.97 84.01 85.56 85.37 43.5 61.92 67.32 71.56 72.12 58.96 68.59 73.92 80.85 81.35
Transcript specificity 6.88 24.84 35.02 56.82 60.04 1.59 9.03 14.26 24.22 24.54 6.96 17.8 26.23 43.96 44.78
Transcript sensitivity 31.68 32.19 35.23 31.8 37.21 26.69 29.43 31.2 32.37 33 48.71 46.71 47.76 42.48 42.25
Transcript F1 score 11.3 28.04 35.12 40.78 45.95 3 13.82 19.57 27.71 28.15 12.18 25.78 33.86 43.21 43.48
Gene specificity 33.16 36.51 63.7 65.67 67.33 17.61 20.16 35.69 40.39 32.79 21.83 26.33 47.43 54.04 52.3
Gene sensitivity 44.77 46.18 50.59 49.33 57.96 28.91 31.79 33.65 34.54 35.05 55.2 55.85 58.03 57.22 57.35
Gene F1 score 38.1 40.78 56.39 56.34 62.29 21.89 24.67 34.64 37.24 33.88 31.29 35.79 52.2 55.58 54.71
  1. Best performance is indicated by bold values