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Table 1 Comparisons between predictions and high-confidence gene sets for Sc. pombe and S. cerevisiae

From: CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

  Nucleotide Exon Intron Gene
  Sn Sp Sn Sp Sn Sp Sn Sp
Sc. pombe (1898/5124 genes in high-confidence set)
CodingQuarry 99.3 99.7 93.4 93.6 94.5 96.7 91.3 89.0
AUGUSTUS 99.2 99.1 92.0 91.4 95.7 92.6 86.9 88.9
TransDecoder 95.4 99.3 84.5 86.3 88.5 97.0 80.2 73.5
S. cerevisiae (5206/6575 genes in high-confidence set)
CodingQuarry 99.2 99.8 90.0 90.0 79.0 67.6 90.4 91.1
AUGUSTUS 97.5 99.7 84.7 90.9 74.4 77.0 85.0 91.5
TransDecoder 92.2 99.5 79.9 74.8 73.9 67.4 80.1 68.0
  1. Sensitivity (Sn) is the proportion of a given feature (nucleotides/exons/introns/genes) in the high-confidence set that are correctly predicted. Specificity (Sp) is the proportion of features in the predicted set that are correct. Sensitivity and specificity calculations for nucleotides are made on nucleotides within coding regions. Further descriptions of these measures are given in the Implementation subsection titled “Quantifying prediction results”. The highest scores in each column for Sc. pombe and S. cerevisiae are shown in boldface.