Figure 4

MAKER2 as a management tool for existing genome annotations. MAKER2 was used to add cross species homology evidence and AED values to six published ant species. These data show how MAKER2 can be used both to add new data to existing datasets and for downstream prioritization of genes in those datasets for further analysis and curation. (A) The Pfam domain content in each AED quartile. Genes receiving higher AED scores are less likely to contain a domain, thus prioritizing them as possible false positive gene predictions. (B) The percent of genes in each AED quartile having an orthologous protein in a related ant species with the average number of orthologs per gene (for the subset of orthologous genes) listed at the bottom. AED score is highly correlated with orthology. (C) The cumulative AED distribution for all six ant species. The spike of genes with AED score at or near 1 suggests potential false positive genes predictions rather than species-specific genes, as these annotations also generally lack EST support and Pfam domains; these gene models are first in MAKER2's list for manual review.