Figure 2

Exon filtering. A) Within Kassiopeia predicted MXE candidates can be filtered by the parameters of the MXE search algorithm and a filter to exclude predicted exons, which overlap with exons of other transcripts or genes. B) The effects of the different filter parameters are demonstrated on the example of a hypothetical gene containing a cluster of four MXEs. The gene includes three exons in its original annotation, exons 1, 2b, and 3 (constitutive exons are displayed as dark grey boxes; light-gray boxes denote introns). The algorithm found alternative exon 2a 5’ of 2b, and the two alternative exons 2c and 2d in the intron between exons 2b and 3. The exon candidates of the cluster of MXEs are drawn in blue. Scores and lengths of the predicted exons are given to demonstrate the potential effect of the filters. Dashed borderlines around MXEs indicate predicted exons that are not present in any annotated isoform, in contrast to continuous lines that indicate exons already annotated in at least one isoform. Exons with a thick borderline were manually verified by EST data, cross-species gene data, or have already been described in the literature.