Figure 9

Human consensus gene prediction accuracy by EVM. The consensus gene prediction accuracy by EVidenceModeler (EVM) is shown based on trained evidence weights and the corresponding combination of evidence, as applied to the GENCODE test regions of the human genome. The accuracies for the inputted gene predictions obtained from the ENCODE Genome Annotation Assessment Project (EGASP) dataset are provided for reference sake, including GENSCAN, TWINSCAN, GlimmerHMM, GeneMark.hmm on the repeat-masked genome, GeneID, and SGPgene. EVM-GF corresponds to EVM applied to these gene prediction tiers alone (GF), and serves as the baseline evidence for the subsequent entries. EVM-GeneWise includes GeneWise predictions based on nonhuman protein homologies; EVM-nap includes AAT-nap spliced alignments of nonhuman proteins; the EVM:gap2_* series includes AAT-gap2 alignments of corresponding transcripts from the Dana Farber Gene Indices (CINGI, Ciona intestinalis [sea squirt]; XGI, Xenopus tropicalis [frog]; GGGI, Gallus gallus [chicken]; DOGGI, Canis familiaris [dog]; SSGI, Sus scrofa [pig]; RGI, rat; MGI, mouse); EVM-alignAsm includes Program to Assemble Spliced Alignments (PASA) alignment assemblies and corresponding terminal exon supplement; and EVM:All includes all evidence described (GF, gap2, nap, GeneWise, and PASA). Sn, sensitivity; Sp, specificity.