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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >RNAiFOLD: A constraint programming algorithm for rna inverse folding and molecular design
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RNAiFOLD: A constraint programming algorithm for rna inverse folding and molecular design

机译：RNAiFOLD：RNA反向折叠和分子设计的约束编程算法

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Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups-for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design-we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver; additionally, the source code can be downloaded from that site.
机译：合成生物学是一门新兴的学科，其长期影响范围从细胞内的单分子检测到合成基因组和新生命形式的创建。通过先驱小组获得了真正惊人的结果，例如，遗传网络的组合合成，使用BioBricks进行的基因组合成以及杂交链反应（HCR），其中稳定的DNA单体仅在暴露于目标DNA片段后才组装，生物分子自身组装途径等。这些工作强烈表明，纳米技术和合成生物学似乎一起构成了21世纪最具变革性的发展。在本文中，我们提出了一种约束编程（CP）方法来解决RNA反折叠问题。给定目标RNA二级结构，我们确定折叠成目标结构的RNA序列。即其最小自由能结构是目标结构。我们的方法代表了RNA设计的一步-我们生产出第一个完整的RNA反折叠方法，该方法可用于各种设计约束条件。我们还引入了一种大型邻域搜索方法，该方法使我们能够以失去完整性为代价来处理大型实例，同时保留满足设计约束条件（图案，GC含量等）的优势。结果表明，我们的软件RNAiFold的性能优于或优于所有最新方法。但是，我们的方法在完整性，灵活性和各种设计约束的支持方面是独一无二的。本文介绍的算法可通过交互式Web服务器公开获得。此外，可以从该站点下载源代码。

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