IN the 80s and 90s members of my laboratory invested considerable energy sequencing what at the time were considered large stretches of mammalian and viral genomes. So I was on somewhat familiar ground when I undertook my first bioinformatics programming project, at the Max Planck Institut für molekulare Genetik in Berlin, working on ‘Der Browser’ — a Java applet for displaying maps of chromosomes being sequenced for the human genome project. This software, by its very nature, involved visualization — my particular area of interest — but also provided me with a salient lesson about human–computer interaction. The programmer (Andrei Grigoriev) who had written the original version of the applet had presented the chromosomes horizontally, a seemingly reasonable decision as this took advantage of the largest area available for presentation in a computer display. However the scientist who directed the further development of Der Browser was a mouse geneticist who was so accustomed to viewing chromosomes in vertical orientation that my initial — and uninspiring — task was to recode the display to provide vertical presentation.
Other aspects of the ‘Der Browser’ project were more inspiring, and I became particularly interested in improving the rudimentary facility for comparing two genomes. On my return to Glasgow, this became the focus of a related desktop application, ‘BugView’, initially designed to allow one to compare the organization of the genomes of virulent and non-virulent strains of bacteria. In fact, one is able to use ‘BugView’ with GenBank files of other genomes, including those containing introns. A description of the application has been published in Bioinformatics (2004) 20:129–130.
In my opinion one of the strengths of ‘BugView’ compared with web-based genome browsers is that it allows the user more control over the input, with quicker response and greater ease of printing and saving output. A limitation is that the program is best used for visual comparison of genomes in which homologous genes have already been identified. Thus, users need to install stand-alone Blast on a Unix machine to prepare a complete sequence comparison of the products of two genomes. Although a Grid facility was set up to provide this as a service to biologists unable to do it themselves, it had to be discontinued when the funding for the overall Grid project came to an end. Science too, has moved on, and genome comparison now frequently involves comparing dozens of genomes rather than the two or three ‘BugView’ can handle. Nevertheless, the software still finds use in genome research, and can be downloaded from the ‘BugView’ web page, where further details may be found.