Table 3 compares the prediction performance of ExAlt-Exon in Table 2 to ExAlt predictions using different parameter settings. The impact of using the gene structure information as input (ExAlt-Exon) was compared to alternatives shown in Table 3 as ExAlt-Frame and ExAlt-Default. ExAlt-Frame makes predictions without using exon coordinates as input but is limited to predicting exons that maintain reading frame consistency with the rest of the known gene. ExAlt-Default is given no gene structure information and checks all three possible reading frames before selecting the exons from the highest scoring reading frame. As expected, starting with an initial known exon improved overall performance, but even when gene structure information is precluded from input, a majority of the exon coordinates were correctly recovered (67% overall).