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This article is part of the supplement: ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011

Open Access Proceedings

Comparative analysis and visualization of multiple collinear genomes

Jeremy R Wang1*, Fernando Pardo-Manuel de Villena2 and Leonard McMillan1

Author Affiliations

1 Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

2 Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

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BMC Bioinformatics 2012, 13(Suppl 3):S13  doi:10.1186/1471-2105-13-S3-S13

Published: 21 March 2012

Abstract

Background

Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research.

Results

We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations.

Conclusions

Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains.