GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

Peter Fischer Hallin, Hans Henrik Stærfeldt, Eva Rotenberg, Tim Terence Binnewies, CJ Benham, David Ussery

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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/].
Original languageEnglish
JournalStandards in Genomic Research
Volume1
Issue number2
Pages (from-to)204-215
ISSN1944-3277
DOIs
Publication statusPublished - 2009

Bibliographical note

This work is licensed under a Creative Commons Attribution 3.0 License.

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