Annotation Condence Score (ACS) is a novel condence scoring system for genome annotation, by comparing annotation of a target genome to a set of selected reference genomes. The system is useful in at least two ways:

1. ACS can be used to "rank" annotation quality of ORFs in the target genome. With a cutoff score for ACS that is determined empirically, annotators can focus only on those with low quality.
2. ACS will be useful to re-evaluate genome annotation periodically and can highlight which annotations need to be revised, thus improving the quality of genome annotation over time.