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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.<\/jats:p><jats:p>Availability and Implementation: 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*\u2264 Python &amp;lt;3.0*, MySQL server &amp;gt;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.<\/jats:p><jats:p>Contact: \u00a0karchin@jhu.edu<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr357","type":"journal-article","created":{"date-parts":[[2011,6,18]],"date-time":"2011-06-18T04:15:07Z","timestamp":1308370507000},"page":"2147-2148","source":"Crossref","is-referenced-by-count":123,"title":["CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer"],"prefix":"10.1093","volume":"27","author":[{"given":"Wing Chung","family":"Wong","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dewey","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Carter","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Diekhans","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael C.","family":"Ryan","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Karchin","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 3In Silico Solutions, Fairfax, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,6,17]]},"reference":[{"key":"2023012511530911400_B1","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1162\/neco.1997.9.7.1545","article-title":"Shape quantization and recognition with randomized trees","volume":"9","author":"Amit","year":"1997","journal-title":"Neural Comput."},{"key":"2023012511530911400_B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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