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Table 2 Accuracy of four methods of gene prediction using the A. thaliana genome

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

  Seqpinga MAKER2b GlimmerHMMc, e AUGUSTUSd
BUSCO 96.44% 94.14% 98.12% 98.64%
CDS Structure Sn 0.2749 0.0738 0.2804 0.3075
Sp 0.8867 0.8877 0.7515 0.7527
Acc 0.5808 0.4808 0.5160 0.5301
Exon structure Sn 0.4596 0.1207 - 0.4155
Sp 0.7313 0.7457 - 0.5373
Acc 0.5955 0.4332 - 0.4764
Nucleotide Level Sn 0.7929 0.1932 0.9350 0.9634
Sp 0.9748 0.9750 0.8150 0.7974
Acc 0.8839 0.5841 0.8750 0.8804
  1. aSeqping: Trained using A. thaliana transcriptome; bMAKER2: SNAP’s A. thaliana HMM, AUGUSTUS’s A. thaliana model and A. thaliana transcriptome; cGlimmerHMM: A. thaliana model; dAUGUSTUS: A. thaliana model
  2. eUsing the available A. thaliana model, GlimmerHMM does not predict exon structure