Figure 5From: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsConsensus 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).Back to article page