SNVBox @ Karchin lab


is a MySQL database that contains pre-computed features for all codons in the human exome, which are found in annotated transcripts and genes (sources are RefSeq, CCDS, Ensembl). The features are properties of amino acid substitutions, regional amino acid sequence composition, multiple sequence alignment-based conservation scores, predicted local structure and annotations of functional regions and sites within proteins. SNVBox can be used as a tool for those developing new computational algorithms to classify amino acid substitutions. Current release is SNVBox 3.0 last updated on 05/01/2014.

SNVBox 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 SNVBox can be used independently of CHASM and VEST software, however these tools use SNVBox as a source of predictive features, and SNVBox currently shares a Wiki site with them.

Documentation for the user

This section provides basic documentation for the user, including instructions to download and install the database. More detail can be found here

Example workflow

Short tutorial on how to use SNVBox with the SNVGet python script. SNVBox queries can be made easier with SNVGet.


Example running SNVBox on real data

Primary citations

If you use SNVBox in a publication, please cite the following:

Wong WC, Kim D, Carter H, Diekhans M, Ryan M and Karchin R (2011) CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer Bioinformatics. 27(15):2147-8

Software primary contact/developer

Rick Kim  rkim at insilico dot us dot com

This is a beta version of the SNVBox documentation page. Please contact the primary developer with feedback, suggestions, and requests to improve this page.