CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments
CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments
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DOI：
10.3390/ijms21113852
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发表时间：
2020-05
影响因子：
5.6
通讯作者：
Martin Raden;Fabio Gutmann;Michael Uhl;R. Backofen
中科院分区：
文献类型：
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作者：
Martin Raden;Fabio Gutmann;Michael Uhl;R. Backofen
在计算机技术中，RNA-RNA相互作用预测被广泛应用于识别可能的相互作用伙伴和评估碱基对解析中的相互作用细节。为了验证特定的相互作用，可以通过补偿性突变实验获得体外证据。不幸的是，补偿性突变的选择不是微不足道的，通常是基于主观的特别决定。为了支持决策过程，我们引入了补偿突变选择器CopomuS。CopomuS使用一套客观标准来评估突变对RNA-RNA相互作用形成的影响，并输出可靠的补偿性突变候选排名。对于RNA-RNA相互作用的评估，使用了最先进的IntaRNA预测工具。我们从文献中研究了成功验证的RNA-RNA相互作用的特征，这指导了CopomuS的设计。最后，我们基于实验验证的原核生物sRNAs及其目标mRNAs的补偿突变来评估其性能。CopomuS预测与已知结果高度一致，使其成为支持RNA-RNA相互作用验证实验设计的有价值的工具。它是IntaRNA包的一部分，可作为独立的Web服务器用于临时应用程序。
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.