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Bioinformatics Advance Access originally published online on April 13, 2006
Bioinformatics 2006 22(13):1569-1576; doi:10.1093/bioinformatics/btl144
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

VizStruct for visualization of genome-wide SNP analyses

Kavitha Bhasi 1, Li Zhang 3, Daniel Brazeau 1, Aidong Zhang 2 and Murali Ramanathan 1,*

1 Department of Pharmaceutical Sciences, State University of New York Buffalo, NY 14260, USA
2 Deparment of Computer Science and Engineering, State University of New York Buffalo, NY 14260, USA
3 Department of Computer Science, Eastern Michigan University Ypsilanti, MI 48197, USA

*To whom correspondence should be addressed.

Motivation: The size, dimensionality and the limited range of the data values make visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for analyzing patterns in SNP datasets.

Results: VizStruct is an interactive visualization technique that reduces multi-dimensional data to two dimensions using the complex-valued harmonics of the discrete Fourier transform (DFT). In the 3D VizStruct extension, the multi-dimensional SNP data vectors are reduced to three dimensions using a combination of the DFT and the Kullback–Leibler divergence. The performance of 3D VizStruct was challenged with several biologically relevant published datasets that included human Chromosome 21, the human lipoprotein lipase (LPL) gene locus and the multi-locus genotypes of coral populations. In every case, the 3D VizStruct mapping provided an intuitive visual description of the key characteristics of the underlying multi-dimensional genotype.

Availability: Excel and MATLAB code are available at http://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/SNP/

Contact: murali{at}Buffalo.edu

Received on March 2, 2006; revised on April 9, 2006; accepted on April 10, 2006

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