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Nucleic Acids Research Advance Access originally published online on December 13, 2007
Nucleic Acids Research 2008 36(1):e3; doi:10.1093/nar/gkm1106
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Nucleic Acids Research, 2008, Vol. 36, No. 1 e3
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Comprehensive viral oligonucleotide probe design using conserved protein regions

Omar J. Jabado1, Yang Liu2, Sean Conlan1, P. Lan Quan1, Hédi Hegyi3, Yves Lussier4, Thomas Briese1, Gustavo Palacios1 and W. I. Lipkin1,*

1Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1801, New York, NY 10032, 2Sigma-Aldrich, Research Biotech, 2909 Laclede Ave, St. Louis, MO 63103, USA, 3Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, PO Box 7, Hungary and 4Center for Biomedical Informatics, Department of Medicine, Section of Genetic Medicine, University of Chicago, 5841 South Maryland Ave, AMB N660B, Chicago, IL 60637, USA

*To whom correspondence should be addressed. Tel: +1 212 342 9031; Fax: +1 212 342 9044; Email: wil2001{at}columbia.edu

Received October 15, 2007. Revised November 26, 2007. Accepted November 27, 2007.

Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.


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