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Welcome to the Karchinlab CHASM wiki. Here you will find information on the following software packages:

CHASM Logo

CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage.

SNV-Box Logo

SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.


Patch v1 for CHASM 3.0 and VEST 3.0 has been released. See Downloads.

Current release is CHASM 3.0, SNVBox 3.0, and VEST 3.0, last updated on 05/22/2014.

Our software is intended for those with substantial bioinformatics and Linux system expertise and access to a large-memory Linux server.

It is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office

If you use our software for a publication, please cite the following references for CHASM.


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CRAVAT Run CHASM directly on the web!


Funding for CHASM and VEST: NIH: U24 CA204817


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