基于量子进化算法的RNA序列-结构比对

RNA Sequence-structural Alignment Based on Quantum Evolutionary Algorithm

多序列比对是计算分子生物学的经典问题,也是许多生物学研究的重要基础步骤.RNA作为生物大分子的一种,不同于蛋白质和DNA,其二级结构在进化过程中比初级序列更保守,因此要求在RNA序列比对中不仅要考虑序列信息,更要着重考虑二级结构信息.提出了一种基于量子进化算法的RNA多序列-结构比对程序,对RNA序列进行了量子编码,设计了考虑进结构信息的全交叉算子,提出了适合于进行RNA序列-结构比对的适应度函数,克服了传统进化算法收敛速度慢和早熟问题.在标准数据库上的测试,证实了方法的有效性.

As a classical problem of computational molecular biology, the multiple sequences alignment is also important foundational process. RNA is one of biological polymer, and is different from protein and DNA that the secondary structure of RNA is more conservative than its primary sequence. Therefore, RNA multiple sequences alignment require not only information of sequences, but also information of secondary structures which those sequences will form. Here, a program QEA-MRNA, which based on quantum evolutionary algorithm（QEA） to align RNA sequences, is proposed. The program introduce a full crossover operator and a fitness function which considering the information of RNA premary sequence controling and the convergent speed. The effectiveness testing cases in BRAliBase. and secondary structure, and improving on prematurity and performance of QEA-MRNA are demonstrated by