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Bioinformatics Advance Access published online on August 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth498
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 6, 2004
Revised August 7, 2004
Accepted August 19, 2004

Article

Filtering of Ineffective siRNAs and Improved siRNA Design Tool

S. M. Yiu 1, Prudence W. H. Wong 2, T. W. Lam 1, Y. C. Mui 1, H. F. Kung 3, Marie Lin 3, Y. T. Cheung 3

1 Department of Computer Science, University of Hong Kong, Hong Kong
2 Department of Computer Science, University of Liverpool, Liverpool L69 7ZF, UK
3 Institute of Molecular Biology, University of Hong Kong, Hong Kong


  Abstract

Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and have many potential applications in therapy, yet how to design an effective siRNA is still not clear. Based on the MPI basic principles (Tuschl et al., 2003), a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs.

Results: The contribution of this paper is two-fold. Firstly, we propose a fair scheme to compare existing design tools based on real data in the literature. Secondly, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective.

Availability: The siRNA design software tool can be found in the website http://www.cs.hku.hk/~sirna/.


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