Finally, the trade off between predicting multiple overlapping exons versus predicting at most one exon per test sequence was measured. With the hold out set comprised of 57% constitutive exons, 18% MS exons, 17% SE exons, and 9% IR exons, both single exon prediction versions of ExAlt (ExAlt-Frame-Single and ExAlt-Default-Single) captured a large percentage of the exons by simply correctly predicting one exon per sequence. When ExAlt is given the coding frame and restricted to predict at most one exon, an exon is correctly predicted in 94% of the sequences (ExAlt-Frame-Single in Table 3). Allowing ExAlt to predict overlapping exons (ExAlt-Frame in Table 3) lowered specificity to 89% but increased the number of correctly annotated exons to 72%. The last three rows show single isoform gene finding performance for N-SCAN, Augustus, and SNAP, which provided an additional point of reference to measure how well conventional gene finders performed in the evaluated gene regions.