sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database
Open Access
- 31 May 2007
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 8 (1), 178
- https://doi.org/10.1186/1471-2105-8-178
Abstract
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 a variety of databases so that the user can verify the uniqueness of the design. We have pre-designed siRNAs for all the known human genes (24,502) in the Refseq database. These siRNAs were pre-BLASTed against the human Unigene database to estimate the target specificity and all results are available online. Conclusion: Although most of the rules for this scoring system were influenced by previously published rules, the weighted scoring system provides better flexibility in designing an appropriate siRNA when compared to the un-weighted scoring system. sIR is not only a comprehensive tool used to design siRNA sequences and lookup pre-designed siRNAs, but it is also a platform where researchers can share information on siRNA design and use.Keywords
This publication has 19 references indexed in Scilit:
- 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targetsNature Methods, 2006
- siRNAs: applications in functional genomics and potential as therapeuticsNature Reviews Drug Discovery, 2004
- Rational siRNA design for RNA interferenceNature Biotechnology, 2004
- Progress in the development of nucleic acid therapeutics for cancer.Cancer Biology & Therapy, 2004
- siRNA technologyMolecular and Cellular Endocrinology, 2004
- Killing the messenger: short RNAs that silence gene expressionNature Reviews Molecular Cell Biology, 2003
- SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression dataNucleic Acids Research, 2003
- Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysateThe EMBO Journal, 2001
- RNA Interference and Small Interfering RNAsChemBioChem, 2001
- Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegansNature, 1998