We describe BugView, a cross-platform application for presenting and comparing the genomes of bacteria or eukaryotes. We give particular emphasis to its use in comparing the genes of related bacterial genomes, and consider different methods of automating the preparation of genome comparison files, including a new web-based facility. Ways of using BugView to study and present the internal structure of genomes are also discussed. BugView/weB, a Java applet for web deployment of BugView files, is presented for the first time.
KeywordsGenome genome comparison genome visualization synteny dynamic programming Java applet
The author would like to thank Micha Bayer and Richard Sinnott of the BRIDGES project for setting up GridBLAST for use with BugView, and all those users who have stimulated improvements by providing feedback on the program.
- 3.Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (2000) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.Google Scholar