Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

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

Jyoti K Shah1, Harold R Garner2345*, Michael A White7, David S Shames1 and John D Minna126

Author Affiliations

1 Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

2 Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

3 Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

4 Center for Biomedical Inventions, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

5 Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

6 Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

7 Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

For all author emails, please log on.

BMC Bioinformatics 2007, 8:178  doi:10.1186/1471-2105-8-178

Published: 31 May 2007

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.