Interpret Protein-Coding and Splicing Variants with MutationForecaster

We are pleased to announce the release of the MutationForecaster v2.0 App in BaseSpace.

MutationForecaster is a suite of tools created by Cytognomix geared to provide researchers with a single interface for genomic variant analysis and validation. The App interprets both protein coding and splicing variants, its strength is in providing the most robust mRNA splicing analysis on the market, presenting three tools created by Cytognomix specifically for this purpose:

ASSEDA – detailed mRNA splicing analysis for individual variants. This tool has been cited in hundreds of articles. This image shows what you might find in the Phenotype Prediction section of ASSEDA results. In this case, a mutation in the exon is abolishing an SF2/ASF site which is a splicing enhancer and is required for exon inclusion.


Shannon Human Splicing Pipeline – mRNA splicing analysis of genome scale input. A VCF file containing up to several million variants can be examined in under 15 minutes generating a ‘short list’ of variants suitable for further laboratory analysis. The Shannon pipeline generates scatterplots to highlight variants which may be of interest. The selected variant in the scatterplot below causes a large increase in predicted cryptic site spliceosome binding affinity.


Veridical – validation of the contribution of variants predicted by the Shannon pipeline to have an influence on mRNA splicing using RNA-Seq files. P-values are computed making use of over one hundred whole-genome control samples. An example of typical Veridical tabular output is shown below.


We also provide EBI – Variant Effect Predictor for analysis of coding sequence changes. Finally, mutations and genes can be filtered and related to peer-reviewed articles containing phenotypes with CytoVA, a unique product which uses advanced visual analytics to expedite literature searching.

Each of these tools can export their results to a database customized for each user. Easily determine the novelty of these variants with an automated search of external databases. This database – as it is based on the Leiden Open Variation Database – presents an interface familiar to some users.

Articles validating each these tools have been published in peer-reviewed journals. Please visit the MutationForecaster homepage for more information and links to these articles. A summary of other tools included in MutationForecaster can be found there as well.

ASSEDA, the Shannon pipeline, and Veridical have been proven to find and validate mRNA splicing variants other traditional methods cannot. Visit the BaseSpace specific summary page for a list of several publications demonstrating this. The link also contains a list of MutationForecaster features available exclusively to BaseSpace users.

The complete set of analyses have been automated with a workflow system, simplifying the user interaction necessary to analyze a set of variants. Any of the tools can be selected to run in sequence and/or simultaneously where possible. While using a workflow, there is no need to wait for the results of one tool before submitting those results to the next tool in the desired pipeline. Results of the each tool present in a workflow can be viewed in a similar way to tools run individually.

Short-term subscriptions are now available on BaseSpace. MutationForecaster can find and validate mutations that others cannot – with advanced, highly cited bioinformatic technologies not available elsewhere.

If you have any questions about MutationForecaster, please contact

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