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www.rnaworkbench.com: A new program for analyzing RNA interference

Radka Svobodová Vařeková,Ivan Bradáč,Martin Plchút,Michal Škrdla,Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer,Heinrich Huber, Gerhard Gierlinger, Ronald Graf,Hakim Tafer,Ivo Hofacker,Peter Schuster,Martin Polčík

Computer Methods and Programs in Biomedicine（2008）

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Abstract
RNA interference (RNAi) has become an important tool to study and utilize gene silencing by introducing short interfering RNA (siRNA). In order to predict the most efficient siRNAs, a new software tool, RNA Workbench (RNAWB), has been designed and is freely available (after registration) on http://www.rnaworkbench.com. In addition to the standard selection rules, RNAWB includes the possibility of statistical analyses of the applied selection rules (criteria). The role of RNA secondary structures in the RNA interference process as well as the application of sequence rules are discussed to show the applicability of the software.
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RNA interference,siRNA design,mRNA secondary structures,siRNA sequence rules
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