title: CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, 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.
authors.affiliation: Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Wing Chung
authors.initials: WC
authors.lastname: Wong
authors.forename: Dewey
authors.initials: D
authors.lastname: Kim
authors.forename: Hannah
authors.initials: H
authors.lastname: Carter
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.forename: Michael C
authors.initials: MC
authors.lastname: Ryan
authors.forename: Rachel
authors.initials: R
authors.lastname: Karchin
mesh_terms: D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D020125:Mutation, Missense; D009369:Neoplasms / Q000235:genetics*; D011381:Programming Languages; D012984:Software