Skip to main content

Poxvirus Bioinformatics

  • Protocol
Vaccinia Virus and Poxvirology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 269))

Abstract

Biochemical and functional analysis of poxvirus genomes, genes, and proteins has entered a new era with the recent sequencing of more than 30 poxvirus genomes. The management and analysis of this volume of sequence data in an efficient and effective manner requires specialized computer software. This chapter describes a number of bioinformatics techniques useful for analyzing poxvirus genomes. Some of the software discussed here have been developed by members of the Poxvirus Bioinformatics Resource Center (PBRC; funded by National Institutes of Health [NIH]) specifically for use with poxvirus genomes. These programs or, more accurately, suites of programs have many functions dedicated to poxvirus genome characterization. Significantly, this software has been designed with ease of use at a single location as the major goal.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Goebel, S. J., Johnson, G. P., Perkus, M. E., Davis, S. W., Winslow, J. P., and Paoletti, E. (1990) The complete DNA sequence of vaccinia virus. Virology 179, 247–266.

    Article  PubMed  CAS  Google Scholar 

  2. Mural, R. J. (2000) ARTEMIS: a tool for displaying and annotating DNA sequence. Brief Bioinform. 1, 199–200.

    Article  PubMed  CAS  Google Scholar 

  3. Sonnhammer, E. L. and Durbin, R. (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167, GC1–GC10.

    Article  PubMed  CAS  Google Scholar 

  4. Wilson, M. D., Riemer, C., Martindale, D. W., Schnupf, P., Boright, A. P., Cheung, T. L., et al. (2001) Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res. 29, 1352–1365.

    Article  PubMed  CAS  Google Scholar 

  5. Huang, X. and Zhang, J. (1996) Methods for comparing a DNA sequence with a protein sequence. Comput. Appl. Biosci. 12, 497–506.

    PubMed  CAS  Google Scholar 

  6. Ehlers, A., Osborne, J., Slack, S., Roper, R. L., and Upton, C. (2002) Poxvirus Orthologous Clusters (POCs). Bioinformatics 18, 1544–1545.

    Article  PubMed  CAS  Google Scholar 

  7. Upton, C., Slack, S., Ehlers, A., and Roper, R. L. (2003) Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome. J. Virol. 77, 7590–6000.

    Google Scholar 

  8. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  9. Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., et al. (2000) PipMaker—a web server for aligning two genomic DNA sequences. Genome Res. 10, 577–586.

    Article  PubMed  CAS  Google Scholar 

  10. Upton, C., Hogg, D., Perrin, D., Boone, M., and Harris, N. L. (2000) Viral genome organizer: a system for analyzing complete viral genomes. Virus. Res. 70, 55–64.

    Article  PubMed  CAS  Google Scholar 

  11. Harris, N. L. (1997) Genotator: a workbench for sequence annotation. Genome Res. 7, 754–762.

    PubMed  CAS  Google Scholar 

  12. Brown, N. P., Leroy, C., and Sander, C. (1998) MView: a web-compatible database search or multiple alignment viewer. Bioinformatics 14, 380–381.

    Article  PubMed  CAS  Google Scholar 

  13. Upton, C. (2000) Screening predicted coding regions in poxvirus genomes. Virus Genes 20, 159–164.

    Article  PubMed  CAS  Google Scholar 

  14. Cattel, K., Koop, B., Olafson, R. S., Fellows, M., Bailey, I., Olafson, R. W., and Upton, C. (2002) Approaches to detection of distantly related proteins by database searches, in BioComputing (Brown, S. M., ed.), Eaton Publishing, Westboro, MA.

    Google Scholar 

  15. Li, W., Pio, F., Pawlowski, K., and Godzik, A. (2000) Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16, 1105–1110.

    Article  PubMed  CAS  Google Scholar 

  16. Upton, C., Mossman, K., and McFadden, G. (1992) Encoding of a homolog of the IFN-gamma receptor by myxoma virus. Science 258, 1369–1373.

    Article  PubMed  CAS  Google Scholar 

  17. Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., and Bairoch, A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235–238.

    Article  PubMed  CAS  Google Scholar 

  18. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.

    Article  PubMed  CAS  Google Scholar 

  19. Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217.

    Article  PubMed  CAS  Google Scholar 

  20. Morgenstern, B., Frech, K., Dress, A., and Werner, T. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14, 290–294.

    Article  PubMed  CAS  Google Scholar 

  21. Morgenstern, B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211–218.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Upton, C. (2004). Poxvirus Bioinformatics. In: Isaacs, S.N. (eds) Vaccinia Virus and Poxvirology. Methods in Molecular Biology, vol 269. Humana Press. https://doi.org/10.1385/1-59259-789-0:347

Download citation

  • DOI: https://doi.org/10.1385/1-59259-789-0:347

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-229-2

  • Online ISBN: 978-1-59259-789-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics