Lu Zhi John, Mathews David H
Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W104-8. doi: 10.1093/nar/gkn250. Epub 2008 May 19.
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.
以mRNA序列作为输入，OligoWalk网络服务器生成一份小干扰RNA（siRNA）候选序列列表，并根据成为有效siRNA（沉默效率大于70%）的概率进行排序。为实现这一点，该服务器预测siRNA与靶mRNA杂交时的自由能变化，同时考虑siRNA和mRNA的自身结构。结构的自由能变化通过配分函数计算进行严格计算。通过更改高级选项，也可以使用不太严格的最低自由能结构或次优结构预测方法来计算自由能变化，以便进行比较。考虑到预测的自由能变化和局部siRNA序列特征，该服务器使用支持向量机以高精度选择有效的siRNA。平均而言，该服务器选择的有效siRNA中能够有效沉默的比例为78.6%。可通过互联网在http://rna.urmc.rochester.edu/servers/oligowalk免费访问OligoWalk网络服务器。
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