Work

Management, presentation and interpretation of genome scans using GSCANDB

Year: 2007

Type: article

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 optimized for analysis of mouse data, but is customizable 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btm123

Authors: Martin Taylor, William Valdar, Ashish Kumar, Jonathan Flint, Richard Mott

Institution: Centre for Human Genetics

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,989

Funders: Wellcome Trust, European Commission