Rapid match-searching for gene silencing assessment
Rapid match-searching for gene silencing assessment
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DOI：
10.1093/bioinformatics/btq318
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发表时间：
2010-08-15
期刊：
影响因子：
5.8
通讯作者：
Waterhouse, Peter M.
中科院分区：
文献类型：
--
作者：
Horn, Mark E. T.;Waterhouse, Peter M.
动机：基因沉默，也称为RNA干扰，需要对沉默者的影响进行可靠的评估。一项关键任务是根据一对多匹配规则（G-U匹配，并提供错配）找到沉默寡聚物与基因组中位点之间的匹配。在设计有效的消声器序列的过程中，需要快速搜索算法来支持消声器影响评估。结果：本文介绍了一种匹配算法和专门用于匹配搜索的数据结构，包括一个内核过程，该内核过程处理称为skyline搜索的数据库任务的布尔版本。除了精确匹配之外，该算法还扩展到适用于植物的特定位置不匹配。计算测试表明，该算法明显快于后缀树替代算法。
Motivation: Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G-U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.Results: The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives.