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Given an mRNA sequence as input, the OligoWalk web server generates a list of small interfering RNA (siRNA) candidate sequences, ranked by the probability of being efficient siRNA (silencing efficacy greater than 70%). To accomplish this, the server predicts the free energy changes of the hybridization of an siRNA to a target mRNA, considering both siRNA and mRNA self-structure. The free energy changes of the structures are rigorously calculated using a partition function calculation. By changing advanced options, the free energy changes can also be calculated using less rigorous lowest free energy structure or suboptimal structure prediction methods for the purpose of comparison. Considering the predicted free energy changes and local siRNA sequence features, the server selects efficient siRNA with high accuracy using a support vector machine. On average, the fraction of efficient siRNAs selected by the server that will be efficient at silencing is 78.6%. The OligoWalk web server is freely accessible through internet at http://rna.urmc.rochester.edu/servers/oligowalk.[1]
RNA interference (RNAi) has emerged as an important tool in science and in medicine. Small-interfering RNAs (siRNAs) can be used to knockdown gene expression of specific mRNAs. In practice, a number of factors influence whether an siRNA sequence will elicit RNAi and knockdown target gene expression. One factor that significantly influences the efficiency of an siRNA is the effect of RNA secondary structure. Self-structure in either the siRNA sequence or the target mRNA at the binding site may prevent gene silencing. This chapter provides protocols for using the OligoWalk software package to design efficient siRNAs. OligoWalk considers the effect of target and guide strand self-structures and also local sequence features in siRNA design. OligoWalk can be run either locally by compiling the software or through a convenient web interface. OligoWalk is freely available at http://rna.urmc.rochester.edu/cgi-bin/server_exe/oligowalk/oligowalk_for... .[2]
