siDRM: an effective and generally applicable online siRNA design tool
siDRM: an effective and generally applicable online siRNA design tool
复制标题
DOI：
10.1093/bioinformatics/btn442
复制
发表时间：
2008-10-15
期刊：
影响因子：
5.8
通讯作者：
Li, Tongbin
中科院分区：
文献类型：
--
作者：
Gong, Wuming;Ren, Yongliang;Li, Tongbin
小干扰RNA（siRNA）已成为研究基因功能不可或缺的工具。大多数现有的 siRNA 设计工具都是在来自有限来源的数据集上进行训练的，这与这些工具最终应用的多样化 siRNA 实验室实践不兼容。我们使用析取规则合并 (DRM) 方法对从 siRecords 编译的大型且多样化的数据集进行了更新的分析，并在新的在线 siRNA 设计工具 siDRM 中实现了生成的规则集。 siDRM 还实现了一些高灵敏度规则集和快速规则集，链接到 siRecords，并使用多个过滤器来检查不需要的有害影响，包括先天免疫反应、细胞毒性效应和选择 siRNA 时的脱靶活动。使用独立数据集进行的性能比较表明，siDRM 在识别有效 siRNA 方面优于 19 种现有 siRNA 设计工具。
Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool. siDRM also implements a few high-sensitivity rule sets and fast rule sets, links to siRecords, and uses several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects and off-target activities in selecting siRNAs. A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs.