Table 2 shows ExAlt's performance on the hold out set compared to the union of different publicly available gene predictions and an initial known exon given as input. This tests the ability to improve an existing annotation, where an initial exon and reading frame are known. Since many test sequences contained multiple overlapping exons, one exon was chosen at random and used as input. Experiments were repeated 10 times and the average taken. Results are listed in Table 2 as ExAlt-Exon for the ExAlt predictions informed by cross-species sequence conservation. Exon sensitivity and specificity are high since at least one predicted exon matched the test exon. For example, in the case of multiple splice site exons with two overlapping exons, a "naive" program predicting only the input exon would achieve 50% sensitivity and 100% specificity. When only a single exon isoform exists the naive program achieves 100% sensitivity and specificity respectively. For the results in Table 2 it was important to compare the decrease in specificity from the naive method in cases where only a single exon isoform occurs versus the gains in sensitivity when multiple overlapping exons occur. Two ab initio single isoform gene finders were included in the comparison, Augustus [34] and SNAP [35]. Also included is the single isoform gene finder, N-SCAN [36], which uses cross-species conservation with Drosophila yakuba, Drosophila pseudoobscura, and Anopheles gambiae [37].