[Filtering of Ineffective siRNAs and Improved siRNA Design Tool.]
>>Bioinformatics. 2004 Aug 27 [Epub ahead of print]
Filtering of Ineffective siRNAs and Improved siRNA Design Tool.
Yiu SM, Wong PW, Lam TW, Mui YC, Kung HF, Lin M, Cheung YT.
Department of Computer Science, University of Hong Kong, Hong Kong.
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 cs.hku.hk;
I believe the nuclear action of these siRNAs is indeed novel; I don't recall seeing anything like that before, nor did a search turn up anything. Interesting, but to echo your thought and paraphrase realtors:
Delivery, Delivery, Delivery!
Cheers, Tuck |
