Advertisement

BugView

A Tool for Genome Visualization and Comparison
  • David P. Leader
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

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.

Keywords

Genome genome comparison genome visualization synteny dynamic programming Java applet 

Notes

Acknowledgments

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.

References

  1. 1.
    Leader, D. P. (2004) BugView: a browser for comparing genomes. Bioinformatics 20, 129–130.CrossRefPubMedGoogle Scholar
  2. 2.
    Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36.CrossRefPubMedGoogle Scholar
  3. 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
  4. 4.
    Grigoriev, A., Levin, A., and Lehrach, H. (1998) A distributed environment for physical map construction. Bioinformatics 14, 252–258.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • David P. Leader
    • 1
  1. 1.Institute of Biomedical and Life Sciences, Division of Biochemistry and Molecular BiologyUniversity of GlasgowGlasgowScotland

Personalised recommendations