GeneWiz Browser: An Interactive Tool for Visualizing Sequenced Chromosomes

Overview

Journal Stand Genomic Sci

Publisher Biomed Central

Specialty Genetics

Date 2011 Feb 10

PMID 21304658

Citations 17

Authors

Peter F Hallin

Hans-Henrik Staerfeldt

Eva Rotenberg

Tim T Binnewies

Craig J Benham

David W Ussery

Affiliations

Soon will be listed here.

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/.

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