dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.
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.
Naito
Yuki
Y
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Yamada
Tomoyuki
T
Matsumiya
Takahiro
T
Ui-Tei
Kumiko
K
Saigo
Kaoru
K
Morishita
Shinichi
S
D000465:Algorithms; D000818:Animals; D020407:Internet; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering