siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
1 Department of Biophysics and Biochemistry, Graduate School of Science and 2 Undergraduate Program for Bioinformatics and Systems Biology, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan and 3 Department 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 3 5841 4407; Fax: +81 3 5841 4400; Email: saigo{at}biochem.s.u-tokyo.ac.jp
Correspondence may also be addressed to Shinichi Morishita. Tel: +81 47 136 3984; Fax: +81 47 136 3977; Email: moris{at}gi.k.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
Received February 15, 2004; Revised and Accepted February 20, 2004
siDirect (http://design.RNAi.jp/) is a web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). Highly effective siRNA sequences are selected using novel guidelines that were established through an extensive study of the relationship between siRNA sequences and RNAi activity. Our efficient software avoids off-target gene silencing to enumerate potential cross-hybridization candidates that the widely used BLAST search may overlook. The website accepts an arbitrary sequence as input and quickly returns siRNA candidates, providing a wide scope of applications in mammalian RNAi, including systematic functional genomics and therapeutic gene silencing.
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