Predicting Genes in Closely Related Species with Scipio and WebScipio

Scipio and WebScipio are homology-based gene prediction software designed for annotating multigenic families and for transferring annotations from one species to closely related species. The strengths include the power to cope with sequencing-related problems such as sequencing errors and assemblies with short contigs but also the ability to correctly predict genes with unusually long introns and/or rather short exons. WebScipio is connected to diArk, the largest collection of eukaryotic genome assemblies, and thereby offers a very convenient way to correct existing annotations and to extend protein family datasets. WebScipio is also a key resource for researchers interested in mutually exclusive splicing, allowing to search for alternative exons not only in introns but also in up- and downstream regions in case of incompleteness of the search sequence. In this chapter, I describe how to use Scipio and WebScipio keeping a first-time user in mind.