Optimizing RNA structures by sequence extensions using RNAcop.
Optimizing RNA structures by sequence extensions using RNAcop.
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DOI：
10.1093/nar/gkv813
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发表时间：
2015-09-30
影响因子：
14.9
通讯作者：
Gorodkin J
中科院分区：
文献类型：
--
作者：
Hecker N;Christensen-Dalsgaard M;Seemann SE;Havgaard JH;Stadler PF;Hofacker IL;Nielsen H;Gorodkin J
RNA二级结构预测的一个关键方面是识别新的功能元件。这是一项具有挑战性的任务，因为这些元件通常嵌入较长的转录物中，其中必须定义元件和侧翼区域之间的边界。侧翼序列在计算分析水平和当元件作为转录本提取用于实验分析时影响功能元件的折叠。在这里，我们分析了不同的侧翼区长度如何影响折叠成一个受约束的结构，通过计算不同大小的侧翼区折叠的概率。我们的方法，Rancop（RNA上下文优化的概率），测试已知的和从头预测的结构。体外实验支持计算分析，并表明，对于一些结构，选择适当长度的侧翼区是至关重要的。Rancop可通过http://rth.dk/resources/rnacop作为Web服务器和独立软件提供。
A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop.