Re-annotation of a portion of the Maize genome using MAKER2. Annotation Edit Distance (AED) provides a measurement for how well an annotation agrees with its associated evidence (see text and Figure 1 for additional details). Shown are cumulative AED distributions for several Maize annotation datasets. Gold curve: AED distribution of high-quality 'gold standard' annotations in the benchmark region that are members of the J. Schnable and M. Freeling Classical Maize Genes List; These genes generally have the lowest AEDs. Red curve: all Maize gene models from the http://www.MaizeSequence.org 5a.59 Working Gene Set in the benchmark region; Blue curve: MAKER2's first pass, de novo annotations for the benchmark region; note that these genes generally have lower AEDs than the 5a.59 Working Gene Set (red curve). Purple curve: automatic MAKER2-based update/revision of the Maize 4a.53 Working Gene Set annotations. Note that the revised dataset now exceeds the quality of the 5a.59 Working Gene Set as judged by AED.