Division of Mathematics, Informatics and Statistics, CSIRO, North Ryde NSW 1670, Australia.
Bioinformatics. 2010 Aug 15;26(16):1932-7. doi: 10.1093/bioinformatics/btq318. Epub 2010 Jul 2.
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.
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.
Source code, executable, data and test results are freely available at ftp://ftp.csiro.au/Horn/RapidMatch.
基因沉默，也称为 RNA 干扰，需要可靠地评估沉默子的影响。一个关键任务是根据一对多的匹配规则（G-U 匹配，允许有不匹配），在沉默子寡聚体和基因组中的位点之间找到匹配。需要快速搜索算法来支持设计有效沉默子序列的程序中的沉默子影响评估。
本文提出了一种专门用于匹配搜索的匹配算法和数据结构，包括一个核心过程，该过程解决了数据库任务的布尔版本，称为天际线搜索。除了精确匹配外，该算法还扩展到允许在植物中使用特定于位置的不匹配。计算测试表明，该算法明显快于后缀树替代方案。
源代码、可执行文件、数据和测试结果可在 ftp://ftp.csiro.au/Horn/RapidMatch 上免费获得。
