SNVBox: database to detect biologically important single nucleotide variants

Case ID:
C11487
Disclosure Date:
3/29/2011
Description:
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 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), 2.5Ã?¢Ã?â? Ã¢â?¬â?? Ã?¢ââ?¬Â°Ã?¤ Python < 3.0Ã?¢Ã?â? Ã¢â?¬â??, MySQL server > 5.0, 60GB available hard disk space (50MB for software and data files, 40GB for MySQL database dump when uncompressed), 2GB of RAM.
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For Information, Contact:
Seth Zonies
szonies1@jhmi.edu
410-614-0300
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