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Table 1 Accuracy of four methods of gene prediction using the O. sativa genome

From: Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data

  Seqpinga MAKER2b GlimmerHMMc AUGUSTUSd, e
BUSCO 95.92% 92.26% 91.53% 88.70%
CDS structure Sn 0.6175 0.5193 0.4394 0.4717
Sp 0.5120 0.4922 0.2774 0.3008
Acc 0.5648 0.5058 0.3584 0.3863
Exon structure Sn 0.4820 0.4028 0.3089 -
Sp 0.4116 0.3880 0.2129 -
Acc 0.4468 0.3954 0.2609 -
Nucleotide Level Sn 0.6906 0.5950 0.6597 0.6581
Sp 0.6484 0.6680 0.4381 0.3698
Acc 0.6695 0.6315 0.5489 0.5140
  1. aSeqping: Trained using rice transcriptome; bMAKER2: SNAP’s rice HMM, AUGUSTUS’s maize model and rice transcriptome; cGlimmerHMM: Trained using rice transcriptome; dAUGUSTUS: maize model
  2. eUsing the available maize models, AUGUSTUS does not predict exon structure