Consensus Gene Structure Prediction by EVM. The main aspects of the EVidenceModeler (EVM) weighted consensus prediction generating algorithm are depicted here, exemplified with a 7 kilobase region of the rice genome. The top view illustrates a genome browser-style view, showing the ab initio gene predictions GlimmerHMM, Fgenesh, and GeneMark.hmm, AAT-gap2 spliced alignments of other plant expressed sequence tags (ESTs), Program to Assemble Spliced Alignments (PASA) assemblies of rice EST and full-length cDNA (FL-cDNA) alignments, AAT-nap spliced alignments of nonrice proteins, and GeneWise protein homology-based predictions. Top strand and bottom strand evidence are separated by the sequence ticker. Evidence is dismantled into candidate introns and exons; candidate exons are shown in the context of the six possible reading frames at the figure bottom. A coding, intron, and intergenic score vector are shown; feature-specific scores (see Materials and methods) were added to corresponding vectors here for illustration purposes only, and note that all introns have feature-specific scores. The selection of exons, introns, and intergenic regions that define the highest scoring path is shown by the connections between exon features within the six-frame feature partition. This highest scoring path yields two complete gene structures, shown as an EVM tier at top, corresponding to the known rice genes (left) LOC_Os03g15860 (peroxisomal membrane carrier protein) and (right) LOC_Os03g15870 (50S ribosomal protein L4, chloroplast precursor).