Figure 3.

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 webcite 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.

Holt and Yandell BMC Bioinformatics 2011 12:491   doi:10.1186/1471-2105-12-491
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