Visual Exploration of Genomic Data

Authors:
Michail Vlachos;Bahar Taneri;Eamonn Keogh;Philip S. Yu
Affiliations:
IBM T.J. Watson Research Center, Hawthorne, NY, USA;Scripps Institute of Oceanography, UCSD, CA, USA;University of California Riverside, CA, USA;IBM T.J. Watson Research Center, Hawthorne, NY, USA
Venue:
PKDD 2007 Proceedings of the 11th European conference on Principles and Practice of Knowledge Discovery in Databases
Year:
2007

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Abstract

In this study, we present methods for comparative visualization of DNA sequences in two dimensions. First, we illustrate a transformation of gene sequences into numerical trajectories. The trajectory visually captures the nucleotide content of each sequence, allowing for fast and easy visualization of long DNA sequences. Then, we project the relative placement of the trajectories on the 2D plane using a spanning-tree arrangement method, which allows the efficient comparison of multiple sequences. We demonstrate with various examples the applicability of our technique in evolutionary biology and specifically in capturing and visualizing the molecular phylogeny between species.