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Detecting circular RNA from high-throughput sequence data with de Bruijn graph
BMC Genomics ( IF 3.5 ) Pub Date : 2020-03-05 , DOI: 10.1186/s12864-019-6154-7
Xin Li , Yufeng Wu

Circular RNA is a type of non-coding RNA, which has a circular structure. Many circular RNAs are stable and contain exons, but are not translated into proteins. Circular RNA has important functions in gene regulation and plays an important role in some human diseases. Several biological methods, such as RNase R treatment, have been developed to identify circular RNA. Multiple bioinformatics tools have also been developed for circular RNA detection with high-throughput sequence data. In this paper, we present circDBG, a new method for circular RNA detection with de Bruijn graph. We conduct various experiments to evaluate the performance of CircDBG based on both simulated and real data. Our results show that CircDBG finds more reliable circRNA with low bias, has more efficiency in running time, and performs better in balancing accuracy and sensitivity than existing methods. As a byproduct, we also introduce a new method to classify circular RNAs based on reads alignment. Finally, we report a potential chimeric circular RNA that is found by CircDBG based on real sequence data. CircDBG can be downloaded from https://github.com/lxwgcool/CircDBG. We develop a new method called CircDBG for circular RNA detection, which is based on de Bruijn graph. We conduct extensive experiments and demonstrate CircDBG outperforms existing tools, especially in saving running time, reducing bias and improving capability of balancing accuracy and sensitivity. We also introduce a new method to classify circular RNAs and report a potential case of chimeric circular RNA.

中文翻译:

使用de Bruijn图从高通量序列数据中检测环状RNA

环状RNA是一种非编码RNA,具有环状结构。许多环状RNA稳定且含有外显子,但不会翻译成蛋白质。环状RNA在基因调控中具有重要作用,并在某些人类疾病中发挥重要作用。已经开发了几种生物学方法,例如RNase R处理来鉴定环状RNA。还开发了多种生物信息学工具,用于通过高通量序列数据进行环形RNA检测。在本文中,我们介绍了circDBG,这是一种用de Bruijn图检测环状RNA的新方法。我们基于模拟和真实数据进行了各种实验,以评估CircDBG的性能。我们的结果表明,CircDBG可以找到更可靠的circRNA,且偏差低,运行时间效率更高,并且在平衡精度和灵敏度方面比现有方法更好。作为副产品,我们还介绍了一种基于读取序列比对环状RNA的新方法。最后,我们报告了CircDBG根据真实序列数据发现的潜在嵌合环状RNA。CircDBG可以从https://github.com/lxwgcool/CircDBG下载。我们开发了一种新的名为CircDBG的环状RNA检测方法,该方法基于de Bruijn图。我们进行了广泛的实验,并证明CircDBG优于现有工具,特别是在节省运行时间,减少偏差以及提高平衡精度和灵敏度的能力方面。我们还介绍了一种对环状RNA进行分类的新方法,并报告了嵌合环状RNA的潜在案例。我们还介绍了一种基于读取序列比对环状RNA的新方法。最后,我们报告了CircDBG根据真实序列数据发现的潜在嵌合环状RNA。CircDBG可以从https://github.com/lxwgcool/CircDBG下载。我们开发了一种新的名为CircDBG的环状RNA检测方法,该方法基于de Bruijn图。我们进行了广泛的实验,并证明CircDBG优于现有工具,特别是在节省运行时间,减少偏差以及提高平衡精度和灵敏度的能力方面。我们还介绍了一种对环状RNA进行分类的新方法,并报告了嵌合环状RNA的潜在案例。我们还介绍了一种基于读数比对对环状RNA进行分类的新方法。最后,我们报告了CircDBG根据真实序列数据发现的潜在嵌合环状RNA。CircDBG可以从https://github.com/lxwgcool/CircDBG下载。我们开发了一种新的名为CircDBG的环状RNA检测方法,该方法基于de Bruijn图。我们进行了广泛的实验,并证明CircDBG优于现有工具,特别是在节省运行时间,减少偏差以及提高平衡精度和灵敏度的能力方面。我们还介绍了一种对环状RNA进行分类的新方法,并报告了嵌合环状RNA的潜在案例。com / lxwgcool / CircDBG。我们开发了一种新的名为CircDBG的环状RNA检测方法,该方法基于de Bruijn图。我们进行了广泛的实验,并证明CircDBG优于现有工具,特别是在节省运行时间,减少偏差以及提高平衡精度和灵敏度的能力方面。我们还介绍了一种对环状RNA进行分类的新方法,并报告了嵌合环状RNA的潜在案例。com / lxwgcool / CircDBG。我们开发了一种新的名为CircDBG的环状RNA检测方法,该方法基于de Bruijn图。我们进行了广泛的实验,并证明CircDBG优于现有工具,特别是在节省运行时间,减少偏差以及提高平衡精度和灵敏度的能力方面。我们还介绍了一种对环状RNA进行分类的新方法,并报告了嵌合环状RNA的潜在案例。
更新日期:2020-03-06
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