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Table 2 Gene model accuracy using unmatched species parameters

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 57.85% 48.62% 43.84% 68.56% 57.96% 73.77%
  Exon Accuracy 30.71% 16.51% 18.58% 53.31% 28.87% 60.11%
D. melanogaster Nucleotide Accuracy 67.47% 66.51% 48.92% 73.78% 72.83% 74.44%
  Exon Accuracy 30.62% 26.25% 19.94% 43.10% 39.74% 53.69%
C. elegans Nucleotide Accuracy 66.18% 67.26% 68.24% 74.32% 71.92% 85.02%
  Exon Accuracy 28.33% 30.01% 35.44% 38.52% 39.42% 63.14%
  1. The effect of limited/insufficient training data on ab initio gene prediction is simulated by providing the algorithms Augustus, GeneMark, and SNAP with incorrect species parameters files (the A. thaliana species parameters were used to produce gene models for C. elegans and D. melanogaster, and the C. elegans parameters were used to produce gene models in A. thaliana). In comparison, the same predictors, when ran as part of the MAKER2 gene annotation pipeline, perform substantially better, even with the same incorrect species parameter files.