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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >Analyzing modular RNA structure reveals low global structural entropy in microrna sequence
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Analyzing modular RNA structure reveals low global structural entropy in microrna sequence

机译:分析模块化RNA结构揭示了microrna序列中较低的整体结构熵

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摘要

Secondary structure remains the most exploitable feature for noncoding RNA (ncRNA) gene finding in genomes. However, methods based on secondary structure prediction may generate superfluous amount of candidates for validation and have yet to deliver the desired performance that can complement experimental efforts in ncRNA gene finding. This paper investigates a novel method, unpaired structural entropy (USE) as a measurement for the structure fold stability of ncRNAs. USE proves to be effective in identifying from the genome background a class of ncRNAs, such as precursor microRNAs (pre-miRNAs) that contains a long stem hairpin loop. USE correlates well and performs better than other measures on pre-miRNAs, including the previously formulated structural entropy. As an SVM classifier, USE outperforms existing pre-miRNA classifiers. A long stem hairpin loop is common for a number of other functional RNAs including introns splicing hairpins loops and intrinsic termination hairpin loops. We believe USE can be further applied in developing ab initio prediction programs for a larger class of ncRNAs.
机译:二级结构仍然是基因组中非编码RNA(ncRNA)基因发现的最可利用的特征。但是,基于二级结构预测的方法可能会生成多余的候选量用于验证,并且尚未提供可与ncRNA基因发现中的实验工作互补的所需性能。本文研究了一种新方法,即不成对结构熵(USE)作为ncRNA结构折叠稳定性的度量。事实证明,USE能有效地从基因组背景中识别出一类ncRNA,例如含有长茎发夹环的前体microRNA(pre-miRNA)。 USE与pre-miRNA的相关性很好,并且比其他措施表现更好,包括先前制定的结构熵。作为SVM分类器,USE的性能优于现有的pre-miRNA分类器。长茎发夹环在许多其他功能性RNA中很常见,包括内含子剪接发夹环和内在终止发夹环。我们相信USE可以进一步用于为更大类别的ncRNA开发从头算预测程序。

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