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Table 1 Gene model accuracy for gene prediction/annotation programs

From: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Reference
Organism
Performance
Category
Ab Initio Predictions MAKER Annotations
   Augustus GeneMark SNAP Augustus GeneMark SNAP
A. thaliana Nucleotide Accuracy 77.04% 74.68% 69.78% 80.53% 79.39% 80.27%
  Exon Accuracy 67.03% 61.31% 56.40% 67.81% 69.60% 68.78%
D. melanogaster Nucleotide Accuracy 76.08% 66.54% 69.29% 76.42% 73.66% 74.33%
  Exon Accuracy 61.37% 47.31% 47.01% 58.56% 58.03% 58.49%
C. elegans Nucleotide Accuracy 88.29% 88.09% 85.10% 87.14% 86.29% 88.48%
  Exon Accuracy 74.62% 68.88% 61.38% 68.60% 65.03% 66.19%
  1. Comparison of gene model accuracies in first-generation genomes for the ab initio gene predictors Augustus, GeneMark, and SNAP in comparison to gene model accuracies produced by the same predictors when ran as part of the MAKER2 gene annotation pipeline.