The coordinates for start and stop codons were included as input to ExAlt but were excluded from input to the gene finders, making it potentially more difficult for the gene finders to accurately predict initial, terminal and single exons. Therefore, for the initial exons to be counted correct, a gene finder was only required to correctly predict the donor site. For terminal exons to be counted correct, a gene finder was only required to correctly predict the acceptor site, and for single gene exons to be counted correct, a gene finder only needed to predict an overlap with the known single exon. The gene finders were run on longer stretches of genomic sequence than ExAlt and have the added challenging task of determining gene boundaries. A gene finder may predict an initial, terminal or single exon to overlap an internal exon in the test set, which would be counted as an incorrect exon prediction. If the start and stop codon information were integrated into the gene finder prediction process, individual prediction performance for the respective gene finders would likely improve. However, since considerable effort has been taken to carefully train and tune the gene finders for annotating long stretches of genomic sequence, the current predictions serve as a reasonable baseline for measuring differences in prediction performance. Using the input exon plus the union of all three single isoform gene finders yields more of the correct multiple splice site exons (71% versus ExAlt's 67%) but at the cost of a large reduction in specificity (64% versus ExAlt's 94%). In the other cases, however, ExAlt matches or improves on the performance of the union of multiple gene finders.