sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database

Background: RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we describe a web-based computational tool, siRNA Information Resource (sIR), which consists of a new open source database that contains validation information about published siRNA sequences and also provides a user-friendly interface to design and analyze siRNA sequences against a chosen target sequence. Results: The siRNA design tool described in this paper employs empirically determined rules derived from a meta-analysis of the published data; it uses a weighted scoring system that determines the optimal sequence within a target mRNA and thus aids in the rational selection of siRNA sequences. This scoring system shows a non-linear correlation with the knockdown efficiency of siRNAs. sIR provides a fast, customized BLAST output for all selected siRNA sequences against ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Jyoti K. Shah, Harold R. Garner, Michael A. White, David S. Shames, John D. Minna
• Keywords: BMCBI 2007, SiRNA Design, SiRNA Design Tool, SiRNA Sequences