We would like to alert readers to the fact that information theory-based splicing mutation analysis has been used to analyze a wide range of variants (in/dels and SNVs) that affect splicing in introns and exons in peer reviewed studies. These tools have been used analyze mutations that alter branchpoint recognition and within introns in peer reviewed studies. The Automated Splice Site and Exon Definition Analysis server, ASSEDA (Mucaki EJ, 2013) analyzes mutations at branchpoints, within intronic sequences, at cryptic splice sites, and at splicing regulatory protein binding sites (“enhancer/silencer” sequences). We have also published the Shannon pipeline (Shirley BC, 2013), which carries out mutation analysis affecting splicing (and transcription factor binding sites; Lu R, 2017) on a genome scale. Veridical is software validates splicing mutations found with the Shannon pipeline (or any other program) with RNASeq data from the same individual (Viner C, 2014, Dorman SN, 2014).
Our previous review article extensively describes the use of these tools for splicing mutation analysis by many other research groups, besides ourselves (Caminsky N, 2014).