Abstract
In recent years, there have been numerous unprecedented technological advances in the field of molecular biology; these include DNA sequencing, mass spectrometry of proteins, and microarray analysis of mRNA transcripts. Perhaps, however, it is the area of genomics, which has now generated the complete genome sequences of more than 100 poxviruses, that has had the greatest impact on the average virology researcher because the DNA sequence data is in constant use in many different ways by almost all molecular virologists. As this data resource grows, so does the importance of the availability of databases and software tools to enable the bench virologist to work with and make use of this (valuable/expensive) DNA sequence information. Thus, providing researchers with intuitive software to first select and reformat genomics data from large databases, second, to compare/analyze genomics data, and third, to view and interpret large and complex sets of results has become pivotal in enabling progress to be made in modern virology. This chapter is directed at the bench virologist and describes the software required for a number of common bioinformatics techniques that are useful for comparing and analyzing poxvirus genomes. In a number of examples, we also highlight the Viral Orthologous Clusters database system and integrated tools that we developed for the management and analysis of complete viral genomes.
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Acknowledgments
The authors thank the many programmers, researchers, and students who have been involved in the development and testing of this software. This work has been supported by NIH/NIAID (Grant AI48653-02 and Contract HHSN266200400036C) and funds from the Natural Sciences Engineering Research Council of Canada. Drs. C. Upton, R. M. L. Buller, and. E. J. Lefkowitz were the original developers of the Poxvirus Bioinformatics Resource.
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Da Silva, M., Upton, C. (2012). Bioinformatics for Analysis of Poxvirus Genomes. In: Isaacs, S. (eds) Vaccinia Virus and Poxvirology. Methods in Molecular Biology, vol 890. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-876-4_14
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DOI: https://doi.org/10.1007/978-1-61779-876-4_14
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