GeneWiz
browser:
An
Interactive
Tool
for Visualizing
Sequenced
Chromosomes

Peter F. Hallin, Hans‐Henrik Stærfeldt, Eva Rotenberg, Tim T. Binnewies, Craig J. Benham, David Wayne Ussery

Abstract


We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot, allowing for example visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. [Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/]

doi:10.4056/sigs.28177



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Announcement

Publication of Standards in Genomic Sciences has been transferred to a new publisher, BioMed Central on behalf of the Genomic Standards Consortium. All submissions to the journal should now be made directly through the BMC website for the journal at: http://www.standardsingenomics.com

Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

SIGS was founded with grants from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707. The journal became self-supporting on October 1, 2011.

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