AcE is a program to aid gene prediction accuracy evaluation. It uses GFF format to make it easy to convert gene prediction results into an analyzable format. Novel features include isoform accuracy evaluation from either the annotated gene or gene prediction perspective or both at the same time. Masking of genomic sequence which has unknown features allows gene predictions in annotated regions to be analyzed in a genomic context. Test sets, such as an artificial sequence test set or genomic context test set, can be generated by selecting specified annotated sequences from a master set.