A Three-Phase Algorithm for Computer Aided siRNA Design

As our knowledge of RNA interference accumulates, it is desirable to incorporate as many selection rules as possible into a computer-aided siRNA-designing tool. This paper presents an algorithm for siRNA selection in which nearly all published siRNA-designing rules are categorized into three groups and applied in three phases according to their identified impact on siRNA function. This tool provides users with the maximum flexibility to adjust each rule and reorganize them in the three phases based on users’ own preferences and/or empirical data. When the generally accepted stringency was set to select siRNA for 23,484 human genes represented in the RefSeq Database (NCBI, human genome build 35.1), we found 1,915 protein-coding genes (8.2%) for which none suitable siRNA sequences can be found. Curiously, among these 1,915 genes, two had validated siRNA sequences published. After close examination of another 105 published human siRNA sequences, we conclude that (A) many of the published siRNA sequences may not be the best for their target genes; (B) some of the published siRNA may risk off-target silencing; and (C) some published rules have to be compromised in order to select a testable siRNA sequence for the hard-to-design genes. Povzetek: Predstavljen je algoritem za obdelovanje genoma.