Abstract
BackgroundGenome 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.ResultsWe 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.ConclusionsUnlike 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.
Highlights
Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others
The tool is used by researchers to perform comparative analysis between 198 common mouse strains
Our tool is well suited for selecting and partitioning strains while simultaneously considering phenotype variation as it relates to a given gene or genomic region
Summary
Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. Existing genome browsers and visualization tools are not wellsuited to perform meaningful comparative analysis among a large number of genomes. Browsers allow biologists to visualize genomic features such as genes, SNPs, CG islands, transcription factor binding sites, and many others and to place these features in their genomic context. They are useful in adding and viewing genome annotations and feature-specific information. Genome browsers support analysis of a single genome, but there is often a need to compare features between one or more genomes. Many visualization methods have been developed to support comparative genomics of animals
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