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Bioinformatics Advance Access published online on March 30, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm123
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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.

Management, presentation and interpretation of genome scans using GSCANDB

Martin Taylor 1,2, William Valdar 1, Ashish Kumar 1, Jonathan Flint 1 and Richard Mott 1,*

1Wellcome Trust Centre for Human Genetics, Roosevelt Drive Oxford OX3 7BN, UK
2Present Address: European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK

*To whom correspondence should be addressed. Richard Mott, E-mail: richard.mott{at}well.ox.ac.uk


  Abstract

Motivation: Advances in high-throughput genotyping have made it possible to carry out genome-wide association studies using very high densities of genetic markers. This has led to the problem of the storage, management, quality control,,presentation and interpretation of results. In order to achieve a successful outcome it may be necessary to analyse the data in different ways and compare the results with genome annotations and other genome scans.

Results: We created GSCANDB, a database for genome scan data, using a MySQL backend and Perl-CGI web interface. It displays genome scans of multiple phenotypes analysed in different ways and projected onto genome annotations derived from EnsMart. The current version is optimised for analysis of mouse data but is customisable to other species.

Availability: Source code and example data are available under the GPL, in versions tailored to either human or mouse association studies, from http://gscan.well.ox.ac.uk/software.

Supplementary Information: The GSCANDB database of mouse genome scans is accessible from http://gscan.well.ox.ac.uk.

Associate Editor: Prof. Dmitrij Frishman

Received on December 18, 2006; revised on March 5, 2007; accepted on March 23, 2007

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