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Bioinformatics Advance Access originally published online on June 28, 2007
Bioinformatics 2007 23(22):3091-3092; doi:10.1093/bioinformatics/btm339
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomic mutation consequence calculator

John E. Major *

Memorial Sloan-Kettering Computational Biology Center, 1275 York Avenue, Box 460, New York, NY 10021, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The genomic mutation consequence calculator (GMCC) is a tool that will reliably and quickly calculate the consequence of arbitrary genomic mutations. GMCC also reports supporting annotations for the specified genomic region. The particular strength of the GMCC is it works in genomic space, not simply in spliced transcript space as some similar tools do. Within gene features, GMCC can report on the effects on splice site, UTR and coding regions in all isoforms affected by the mutation. A considerable number of genomic annotations are also reported, including: genomic conservation score, known SNPs, COSMIC mutations, disease associations and others. The manual interface also offers link outs to various external databases and resources. In batch mode, GMCC returns a csv file which can easily be parsed by the end user.

Audience: GMCC is intended to support the many tumor resequencing efforts, but can be useful to any study investigating genomic mutations.

Availability: GMCC is freely available via a web portal with a manual mode and a batch query mode. It may be found at this URL: http://cbio.mskcc.org/gmcc

Contact: majorj{at}mskcc.org

Supplementary information: A FAQ and examples can be found at the URL above.

Associate Editor: John Quackenbush

Received on May 15, 2007; revised on June 19, 2007; accepted on June 19, 2007

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