Multi-objective genetic algorithm for pseudoknotted RNA sequence design.
Multi-objective genetic algorithm for pseudoknotted RNA sequence design.
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DOI：
10.3389/fgene.2012.00036
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发表时间：
2012
影响因子：
3.7
通讯作者：
Taneda A
中科院分区：
文献类型：
--
作者：
Taneda A
RNA 反向折叠是一种计算技术，用于设计折叠成用户指定的二级结构的 RNA 序列。尽管假结是 RNA 结构中功能上重要的基序，但与无假结 RNA 设计相比，有关假结 RNA 反向折叠的报道较少。在本文中，我们提出了多目标遗传算法（MOGA）的新版本 MODENA，我们之前曾提出该算法用于无假结 RNA 逆折叠。在新版本的 MODENA 中，(i) 实现了新的交叉算子，(ii) 伪结预测方法 IPknot 和 HotKnots 用于评估设计的 RNA 序列，使我们能够执行伪结 RNA 的逆折叠。具有新交叉算子的新版本 MODENA 与由天然假结 RNA 二级结构组成的数据集进行了基准测试，我们发现与其他假结设计算法相比，MODENA 可以成功设计更多的假结 RNA。此外，通过设计折叠成丁型肝炎病毒核酶假结结构的RNA序列，测试了新版MODENA中新实现的序列约束功能；结果，我们成功设计了八个RNA序列。新版本的 MODENA 可从 下载。
RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding. In the new version of MODENA, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, IPknot and HotKnots, are used to evaluate the designed RNA sequences, allowing us to perform the inverse folding of pseudoknotted RNAs. The new version of MODENA with the new crossover operator was benchmarked with a dataset composed of natural pseudoknotted RNA secondary structures, and we found that MODENA can successfully design more pseudoknotted RNAs compared to the other pseudoknot design algorithm. In addition, a sequence constraint function newly implemented in the new version of MODENA was tested by designing RNA sequences which fold into the pseudoknotted structure of a hepatitis delta virus ribozyme; as a result, we successfully designed eight RNA sequences. The new version of MODENA is downloadable from .