title: siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.
abstract: 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.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Naito
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Yamada
authors.forename: Kumiko
authors.initials: K
authors.lastname: Ui-Tei
authors.forename: Shinichi
authors.initials: S
authors.lastname: Morishita
authors.forename: Kaoru
authors.initials: K
authors.lastname: Saigo
mesh_terms: D000465:Algorithms; D000818:Animals; D020407:Internet; D008322:Mammals / Q000235:genetics; D008969:Molecular Sequence Data; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry*; D012984:Software
chemical_list: D034741:RNA, Small Interfering