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

ABSTRACT: 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.

SUBMITTER: Naito Y 

PROVIDER: S-EPMC1160180 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature

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

Naito Yuki Y   Yamada Tomoyuki T   Matsumiya Takahiro T   Ui-Tei Kumiko K   Saigo Kaoru K   Morishita Shinichi S  

Nucleic acids research 20050701 Web Server issue

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  ...[more]

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