Bioinformatics for Analysis of Poxvirus Genomes

Part of the Methods in Molecular Biology book series (MIMB, volume 890)


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.

Key words

Poxvirus Vaccinia virus Smallpox Bioinformatics Genomics Dotplot Multiple sequence alignment VOCs VGO BLAST JDotter MSA 



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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Biochemistry and MicrobiologyUniversity of VictoriaVictoriaCanada

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