Design of RNAs: comparing programs for inverse RNA folding.
Design of RNAs: comparing programs for inverse RNA folding.
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DOI：
10.1093/bib/bbw120
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发表时间：
2018-03-01
影响因子：
9.5
通讯作者：
Barash D
中科院分区：
文献类型：
--
作者：
Churkin A;Retwitzer MD;Reinharz V;Ponty Y;Waldispühl J;Barash D
在过去的几年中，用于预测具有所需折叠特性的RNA序列的计算程序已经得到了广泛的开发和扩展。给定二级结构，这些程序旨在预测折叠成目标最小自由能二级结构的序列，同时考虑各种约束。这个过程被称为反向RNA折叠。反向RNA折叠传统上用于设计具有有利性质的优化RNA，鉴于合成生物学和RNA纳米结构的不断扩大的新领域的进展，预计该应用在未来将大幅增长。此外，它最近被证明，反向RNA折叠可以成功地用作一个有价值的预处理步骤，在计算检测新的非编码RNA。这篇评论介绍了最流行的免费软件程序，已开发用于这样的目的，从RNAinverse，制定反向RNA折叠问题时设计的。最近发表的考虑RNA二级结构作为输入的是antaRNA，RNAiFold和incaRNAfbinv，每个都具有不同的特征，可以在实践中有益于特定的生物学问题。各种程序还使用不同的方法，从蚁群优化到约束编程，以及自适应行走，模拟退火和玻尔兹曼采样。这篇评论比较了各种方案，并提供了一个简单的描述，将有利于从业人员选择最合适的方案的各种可能性。它是面向特定的任务，需要RNA设计的基础上输入的二级结构，展望未来的RNA设计程序。
Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.
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