AVISPA’s analysis pipeline. The analysis is composed of the following steps. (1) Query submission: users submit a query composed of either a single exon of interest or an exon triplet that also specifies the up- and downstream exons. (2) Query matching: the submitted query is first matched against internal databases (DB) of known transcripts and alternative exons. If no match is found the query is searched against the reference genome. If the query cannot be matched (red cross) an error is reported. (3) Splicing prediction: a successfully matched query (light blue rectangle) is scored as an alternative cassette exon, followed by scoring for differential splicing in four tissue groups. (4) Splicing analysis: if the query’s predictions pass a user-defined significance threshold a splicing analysis is performed. Analysis includes feature enrichment, effect of in silico motif removal on splicing predictions, and mapping putative regulatory motifs to the genome. A visual summary of both predictions and splicing analysis is produced (right).