Prediction of common secondary structures of RNAs: a genetic algorithm approach
Prediction of common secondary structures of RNAs: a genetic algorithm approach
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DOI：
10.1093/nar/28.4.991
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发表时间：
2000-02-15
影响因子：
14.9
通讯作者：
Maizel, JV
中科院分区：
文献类型：
--
作者：
Chen, JH;Le, SY;Maizel, JV
在这项研究中，我们将遗传算法应用于一组RNA序列，以寻找共同的RNA二级结构。我们的方法是分三步走。在程序的第一阶段，对于每个序列，使用遗传算法将种群中的结构优化到一定程度的稳定性。在这一步中，结构的自由能是算法的适应度标准。接下来，对于每个结构，我们定义了相对于其他序列中的那些结构保守的措施。我们将这一度量用于遗传算法中，以提高序列群体中结构的序列之间的结构相似性。最后，我们选择那些满足一定结构稳定性和相似性条件的结构作为一组RNA序列的预测共同结构。我们分别对一组tRNA、5S rRNA、HIV-1的REV反应元件(RRE)和HIV-2/SIV的RRE进行了检测，获得了满意的结果。
In this study we apply a genetic algorithm to a set of RNA sequences to find common RNA secondary structures. Our method is a three-step procedure. At the first stage of the procedure for each sequence, a genetic algorithm is used to optimize the structures in a population to a certain degree of stability. In this step, the free energy of a structure is the fitness criterion for the algorithm. Next, for each structure, we define a measure of structural conservation with respect to those in other sequences. We use this measure in a genetic algorithm to improve the structural similarity among sequences for the structures in the population of a sequence. Finally, we select those structures satisfying certain conditions of structural stability and similarity as predicted common structures for a set of RNA sequences. We have obtained satisfactory results from a set of tRNA, 5S rRNA, rev response elements(RRE) of HIV-1 and RRE of HIV-2/SIV, respectively.