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Comparative Genomics pp 109–132Cite as

BugView

A Tool for Genome Visualization and Comparison

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Part of the book series: Methods in Molecular Biology™ ((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.

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References

  1. Leader, D. P. (2004) BugView: a browser for comparing genomes. Bioinformatics 20, 129–130.

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  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.

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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.

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Authors and Affiliations

  1. Institute of Biomedical and Life Sciences, Division of Biochemistry and Molecular Biology, University of Glasgow, Glasgow, Scotland

    David P. Leader

Authors
  1. David P. Leader
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Editor information

Editors and Affiliations

  1. Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI

    Nicholas H. Bergman

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© 2007 Humana Press Inc.

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Leader, D.P. (2007). BugView. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_7

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  • DOI: https://doi.org/10.1007/978-1-59745-514-5_7

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-693-1

  • Online ISBN: 978-1-59745-514-5

  • eBook Packages: Springer Protocols

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