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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