Evolutionary solution for the RNA design problem
Evolutionary solution for the RNA design problem
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DOI：
10.1093/bioinformatics/btu001
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发表时间：
2014-05-01
期刊：
影响因子：
5.8
通讯作者：
Mohammad-Noori, Morteza
中科院分区：
文献类型：
--
作者：
Esmaili-Taheri, Ali;Ganjtabesh, Mohammad;Mohammad-Noori, Morteza
动机：RNA在细胞过程中起着重要作用。RNA的功能高度依赖于其3D构象，这被称为RNA三级结构。由于这些结构的预测或实验测定是困难的，所以许多工作集中在与RNA二级结构相关的问题上。在这里，我们考虑RNA逆折叠问题，其中RNA二级结构作为目标结构，目标是设计折叠成目标结构的RNA序列。在这篇文章中，我们介绍了一种新的进化算法的RNA逆折叠问题。我们的算法，题为进化RNA设计，产生一个序列的最小自由能结构是相同的目标structure.Results：我们比较了我们的算法与INFO-RNA，MODENA，RNAiFold和NUPACK方法的一些生物测试集。结果表明，对于较长的结构，该算法在能量范围、准确度、加速比和核苷酸分布等方面都优于其他算法。特别地，在我们的方法中生成的RNA序列更加可靠，并且与天然RNA序列相似。
Motivation: RNAs play fundamental roles in cellular processes. The function of an RNA is highly dependent on its 3D conformation, which is referred to as the RNA tertiary structure. Because the prediction or experimental determination of these structures is difficult, so many works focus on the problems associated with the RNA secondary structure. Here, we consider the RNA inverse folding problem, in which an RNA secondary structure is given as a target structure and the goal is to design an RNA sequence that folds into the target structure. In this article, we introduce a new evolutionary algorithm for the RNA inverse folding problem. Our algorithm, entitled Evolutionary RNA Design, generates a sequence whose minimum free energy structure is the same as the target structure.Results: We compare our algorithm with INFO-RNA, MODENA, RNAiFold and NUPACK approaches for some biological test sets. The results presented in this article indicate that for longer structures, our algorithm performs better than the other mentioned algorithms in terms of the energy range, accuracy, speedup and nucleotide distribution. Particularly, the generated RNA sequences in our method are much more reliable and similar to the natural RNA sequences.