BugView

A Genome Browser for the Desktop

Introduction

‘BugView’ is a genome browser for comparing the arrangement of genes on a pair of related genomes, although it can also be used to view individual genomes. It was written for comparative studies of bacterial genomes — hence the name — although it handles intron-containing eukaryotic chromosomes equally well. As a desktop application, rather than a web facility, ‘BugView’ is responds quickly to adjustment of the visualization, the user has control over file input (GenBank format is used), and views of the genomes can easily be printed or saved. The desktop application has a rich feature feature set, and was the sole focus of development. More recently, however, a web version (a Java applet) has been produced for use in teaching etc.

Click on the thumbnails below for screen-shots illustrating some of the visualizations that ‘BugView’ provides.

Comparison of bacterial genomes

 

Documentation

‘BugView’ has a brief set of internal Help menu items, with full documentation in the form an illustrated manual available as a pdf file that can either be downloaded or viewed on-line .

A short description of ‘BugView’ was published as an application note in Bioinformatics (2004) 20, 129-130. It was also discussed, with further illustrations of its use, in The Biochemist (2004) 26, 7-11. There is a more extensive article about ‘BugView’ in Methods in Molecular Biology (2007) 395, 109–132, which includes a description of the applet version. (The Grid facility mentioned in that article is, unfortunately, no longer available.)

Downloads

‘BugView’ is available for platforms running Java 1.1 and above. Select the appropriate version for your operating system, below:

It helps to read the manual before using the program:

The Perl script, gcfprep, used in conjunction with standalone BLAST from NCBI, is also available.

The Applet version of the software, ‘BugView Web’, can be downloaded here.

Authorship and Acknowledgement

‘Bug View’ was developed by David P. Leader. It incorporates some code written by Andrei Grigoriev for the original ‘Der Browser’ Java applet.