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Figure 7 | Genome Biology

Figure 7

From: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Figure 7

Rice consensus gene prediction accuracy using optimized evidence weights. Gene prediction accuracy for EVidenceModeler (EVM) was calculated at the nucleotide, exon, and complete gene level using trained weights and specific sets of evidence, applied to 500 of the reference rice gene structures. The evidence evaluated is described as follows: EVM:GF includes ab initio gene predictions (GF) alone; EVM:GF+gap2 includes GF plus the AAT-gap2 alignments of other plant expressed sequence tags (gap2); EVM:GF+nap includes GF plus AAT-nap alignments of nonrice proteins (nap); EVM:GF+GeneWise includes GF plus the GeneWise predictions based on nonrice protein homologies (GeneWise); EVM:ALL(-PASA) includes GF, nap, gap2, and GeneWise; EVM:ALL(+PASA) additionally includes the Program to Assemble Spliced Alignments (PASA) alignment assemblies and PASA long-open reading frame (ORF)-based terminal exon supplement. Sn, sensitivity; Sp, specificity.

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