Activity diagram of the search algorithm. The activity diagram shows the processing steps of the search algorithm and the influence of the parameters on each step. The run starts with an exon-intron gene structure determined by Scipio. Based on the chosen parameters the exons and corresponding introns are selected and searched for mutually exclusive spliced exon candidates. The candidates are processed and filtered. These steps are repeated in the case of a recursive run. In the end, the algorithm outputs the exon-intron structure including mutually exclusive spliced exons.