Fig. 4

Illustration of the paralog-to-contig assignment for arrestin paralogs in pufferfish (a) and latrophilin paralogs in cod (b). All known zebrafish paralogs of the respective families were used as queries. Homologous coding exons that were detected by the EMS-pipeline and Scipio, resp., are shown as black open boxes on their respective contigs (grey boxes). Putatively missing (or deleted) coding exons are denoted by dotted boxes. False positive TCE-hits that were included in the ExonMatchSolver-solution, but not annotated by the spliced alignment tool are indicated by light green boxes. False positives appearing in the final output of either tool are indicated by brown boxes. The solution of the EMS-pipeline considering all of its stages is highlighted by broad blue paths in the back of the exons. Scipio’s best scoring proposition for each query is illustrated as colored dots and paths. In addition, true positive TCEs that were detected by the ExonMatchSolver, but not by the spliced alignment tool, are marked with an asterisk (*). Note that Scipio with cross-species default options did not propose any hit for ARR3b. GS genescaffold, c contig, s scaffold, TCE translated coding exon