Table 1

Gene model accuracy for gene prediction/annotation programs

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%


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.

Holt and Yandell BMC Bioinformatics 2011 12:491   doi:10.1186/1471-2105-12-491

Open Data