Human Splicing Finder: an online bioinformatics tool to predict splicing signals

TLDR

Millions of mutations are identified yearly, and an increasing proportion are believed to affect mRNA splicing by altering splice sites or auxiliary cis‑splicing sequences. The authors developed Human Splicing Finder (HSF) to predict mutation effects on splicing signals and identify splicing motifs in human sequences. HSF incorporates all available auxiliary sequence matrices, new PWMs for 5′/3′ splice sites and branch points, and binding site matrices for 9G8, Tra2‑β, and hnRNP A1, and was benchmarked on 83 intronic and 35 exonic mutations. HSF correctly predicted mutation effects in almost all tested cases, making it a valuable resource for research, diagnostics, therapeutic exon skipping, and large‑scale projects such as GEN2PHEN and the Human Variome Project.

Abstract

Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. We also developed new Position Weight Matrices to assess the strength of 5′ and 3′ splice sites and branch points. We evaluated HSF efficiency using a set of 83 intronic and 35 exonic mutations known to result in splicing defects. We showed that the mutation effect was correctly predicted in almost all cases. HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project.