Skip Navigation



Bioinformatics Advance Access published online on June 28, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm339
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
23/22/3091    most recent
btm339v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Major, J. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Major, J. E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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 1,*

1Memorial Sloan-Kettering Computational Biology Center, 1275 York Avenue, Box 460, New York, NY 10021, USA

*To whom correspondence should be addressed. John E. Major, E-mail: majorj{at}mskcc.org


  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

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

Associate Editor: Prof. John Quackenbush

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.