基于茎区组合的RNA二级结构预测算法.pdfVIP

第 30 卷第 6期 计算机应用 Vo.l 30 No. 6 2010年 6月 Journal of ComputerApp li ations June 2010 : 100 1- 9081( 20 10) 06- 1694- 04 RNA 骆嘉伟, 陈 涛 ( , 410082) ( springpaul@ 139. om ) : RNA 二级结构预测是生物信息学的研究热点和难点, 特别是对于含假结的 RNA 二级结构的预测, 已 被证明是NP 问题根据 RNA 折叠的特点, 提出了一种基于茎区组合的智能优化算法来预测 RNA 的二级结构该 算法以 RNA 的茎区为基本单元, 结合图论思想, 通过二元关系的基本理论, 依据自由能最小原则获取茎区的最优组 3 2 合该算法的时间复杂度为O ( n ), 空间复杂度为 O (n ), 而且可以发现假结实验结果证明了算法的有效性 : RNA 二级结构; 茎区; 假结; 拟序集; 极大链 : TP30 1. 6 : A RNA secondary structure p rediction algorithm based on steam com b ination LUO Jiaw ei, CHEN Tao (School of Comp uter and Comm unication, H unan University, ChangshaH unan 410082, China) A bstract: RNA se ondary stru ture pred i tion is the hot topi in b ioin form ati s. E spe ially, the RNA se ondary stru ture pred i tion w ith pseudoknot has been proved a NPhard prob lem. A ording to the hara teristi s of RNA fold ing, a heuristi algorithm QuasiRP to pred i t RNA se ondary stru ture w as presented. Using stem as the un it, omb in ing graph theory and fundam ental theory of binary relations, QuasiRP an find the optmi al stem omb ination based on M inmi al Free 3 2 Energy (MFE) riterion. The tmi e om plex ity is O( n ) wh ile the spa e omp lex ity isO ( n ), and pseudoknot an be found. The resu lts show the validit