siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference | Zendy

Yuki Naito | Zendy; Toshimichi Yamada | Zendy; Kumiko UiTei | Zendy; Shinichi Morishita | Zendy; K. Saigo | Zendy

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siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference

Author(s) -

Yuki Naito,

Toshimichi Yamada,

Kumiko UiTei,

Shinichi Morishita,

K. Saigo

Publication year - 2004

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkh442

Subject(s) - rna interference , biology , gene silencing , small interfering rna , functional genomics , trans acting sirna , computational biology , rna silencing , interference (communication) , genetics , gene , rna , genomics , genome , computer science , computer network , channel (broadcasting)

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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