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Nucleic Acids Research 2006 34(Web Server issue):W448-W450; doi:10.1093/nar/gkl214
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences

Yuki Naito1,*, Kumiko Ui-Tei1,2, Toru Nishikawa3, Yutaka Takebe4 and Kaoru Saigo1

1 Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 2 Undergraduate Program for Bioinformatics and Systems Biology, School of Science, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 3 Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 4 Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan

*To whom correspondence should be addressed. Tel: +81 3 5841 4404; Fax: +81 3 5841 4400; Email: y-naito{at}RNAi.jp

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

siVirus (http://siVirus.RNAi.jp/) is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. These siRNAs are expected to resist viral mutational escape, since their highly conserved targets likely contain structurally/functionally constrained elements. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health.


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