Human Splicing Finder (HSF)

About the resource

Type of resource: Variant prediction system
License/availability:
Website: Click here to view website
User documentation: Click here to view documentation
Relevant publication:

Description

The Human Splicing Finder (HSF) system combines twelve different algorithms to identify and predict the effect of a mutation on splicing motifs including the accept and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).

The HSF (Human Splice Finder) system has quickly become an international reference. Because of the complexity of splicing signals users are facing a flow of information, which is difficult to handle by non-specialists. To make this information accessible to all we have created an expert system for data interpretation. This algorithm uses a decision tree based on mutation position: intronic vs. exonic; localization in wild type splice sites or branch point; activation of cryptic splice sites; alteration/creation of ESE/ESS (exonic splicing enhancer / exonic splicing silencer). Based on these criteria, context-irrelevant signals are automatically ruled out to focus on relevant ones to evaluate the potential impact of mutations.
Furthermore, to allow implementation of the HSF system in NGS (Next Generation Sequencing) pipelines, we developed dedicated Web services. They are able to process genomic variations, handle VCF files, and provide results in JSON format.

Thanks to its expert system, we believe that, in the NGS era, HSF is a masterpiece system that should be included in all bioinformatics pipelines. It could be combined with other systems such as the UMD-Predictor to predict the consequences of all types of mutations.

The web interface is useful: for rapid analysis through its expert system; for splicing signals discovery in any human sequence; for identification of exonic splicing profiles to design antisense oligonucleotides to induce exon skipping.