CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17.


Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline.

Availability and implementation: MySQL database, source code and binaries freely available for academic/government use at, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • DNA Mutational Analysis / methods*
  • Databases, Factual
  • Humans
  • Mutation, Missense
  • Neoplasms / genetics*
  • Programming Languages
  • Software*