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Nucleic Acids Research 2005 33(Web Server Issue):W589-W591; doi:10.1093/nar/gki419
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference

Yuki Naito1, Tomoyuki Yamada3, Takahiro Matsumiya3, Kumiko Ui-Tei1,2, Kaoru Saigo1 and Shinichi Morishita3,*

1Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 2Undergraduate Program for Bioinformatics and Systems Biology, School of Science, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 3Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan

*To whom correspondence should be addressed. Tel: +81 47 136 3984; Fax: +81 47 136 3977; Email: moris{at}k.u-tokyo.ac.jp

Received February 14, 2005. Revised March 21, 2005. Accepted March 21, 2005.

Off-target effects are one of the most serious problems in RNA interference (RNAi). Here, we present dsCheck (http://dsCheck.RNAi.jp/), web-based online software for estimating off-target effects caused by the long double-stranded RNA (dsRNA) used in RNAi studies. In the biochemical process of RNAi, the long dsRNA is cleaved by Dicer into short-interfering RNA (siRNA) cocktails. The software simulates this process and investigates individual 19 nt substrings of the long dsRNA. Subsequently, the software promptly enumerates a list of potential off-target gene candidates based on the order of off-target effects using its novel algorithm, which significantly improves both the efficiency and the sensitivity of the homology search. The website not only provides a rigorous off-target search to verify previously designed dsRNA sequences but also presents ‘off-target minimized’ dsRNA design, which is essential for reliable experiments in RNAi-based functional genomics.

Correspondence may also be addressed to Kumiko Ui-Tei. Tel: +81 3 5841 3044; Fax: +81 3 5841 3044; Email: ktei{at}biochem.s.u-tokyo.ac.jp

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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