Filtering of Ineffective siRNAs and Improved siRNA Design Tool
Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been develope...
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| Veröffentlicht in: | Bioinformatics 2005-01, Vol.21 (2), p.144-151 |
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| container_title | Bioinformatics |
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| creator | Yiu, S. M. Wong, Prudence W. H. Lam, T.W. Mui, Y.C. Kung, H. F. Lin, Marie Cheung, Y. T. |
| description | Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, 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 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, 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/ Contact: smyiu@cs.hku.hk |
| doi_str_mv | 10.1093/bioinformatics/bth498 |
| format | Article |
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M. ; Wong, Prudence W. H. ; Lam, T.W. ; Mui, Y.C. ; Kung, H. F. ; Lin, Marie ; Cheung, Y. T.</creator><creatorcontrib>Yiu, S. M. ; Wong, Prudence W. H. ; Lam, T.W. ; Mui, Y.C. ; Kung, H. F. ; Lin, Marie ; Cheung, Y. T.</creatorcontrib><description>Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, 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 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, 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. 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M.</creatorcontrib><creatorcontrib>Wong, Prudence W. H.</creatorcontrib><creatorcontrib>Lam, T.W.</creatorcontrib><creatorcontrib>Mui, Y.C.</creatorcontrib><creatorcontrib>Kung, H. F.</creatorcontrib><creatorcontrib>Lin, Marie</creatorcontrib><creatorcontrib>Cheung, Y. T.</creatorcontrib><title>Filtering of Ineffective siRNAs and Improved siRNA Design Tool</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, 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 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, 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/ Contact: smyiu@cs.hku.hk</description><subject>Algorithms</subject><subject>Artificial Intelligence</subject><subject>Base Sequence</subject><subject>Benchmarking - methods</subject><subject>Biological and medical sciences</subject><subject>Computer-Aided Design</subject><subject>Fundamental and applied biological sciences. 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M.</au><au>Wong, Prudence W. H.</au><au>Lam, T.W.</au><au>Mui, Y.C.</au><au>Kung, H. F.</au><au>Lin, Marie</au><au>Cheung, Y. T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Filtering of Ineffective siRNAs and Improved siRNA Design Tool</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2005-01-15</date><risdate>2005</risdate><volume>21</volume><issue>2</issue><spage>144</spage><epage>151</epage><pages>144-151</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><coden>BOINFP</coden><abstract>Motivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, 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 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, 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. 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| subjects | Algorithms Artificial Intelligence Base Sequence Benchmarking - methods Biological and medical sciences Computer-Aided Design Fundamental and applied biological sciences. Psychology General aspects Genetic Engineering - methods Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Chemical Models, Molecular Molecular Sequence Data RNA, Small Interfering - chemistry RNA, Small Interfering - classification RNA, Small Interfering - genetics Sequence Alignment - methods Sequence Analysis, RNA Software |
| title | Filtering of Ineffective siRNAs and Improved siRNA Design Tool |
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