CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
Bioinformatics
; 27(15): 2147-8, 2011 Aug 01.
Article
em En
| MEDLINE
| ID: mdl-21685053
ABSTRACT
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 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.
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Software
/
Análise Mutacional de DNA
/
Neoplasias
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Estados Unidos