Real-time audio and visual display of the Coronavirus genome.
Real-time audio and visual display of the Coronavirus genome.
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冠状病毒基因组的实时音频和视频显示。
DOI：
10.1186/s12859-020-03760-7
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发表时间：
2020-10-02
影响因子：
3
通讯作者：
Temple MD
中科院分区：
文献类型：
--
作者：
Temple MD
本文描述了一个基于网络的工具，它结合了发声和动画显示来查询SARS-CoV-2基因组。音频数据是从各种已知在RNA功能中重要的RNA基序中实时生成的。此外，还使用了与RNA翻译和转录相关的元数据来塑造听觉和视觉显示。这些工具共同为进一步了解病毒RNA基因组的新陈代谢提供了一种独特的方法。除了传统的书面和可视方法外，该音频还提供了另一种表示RNA功能的方法。SARS-CoV-2基因组RNA序列的声学作用产生了一个复杂的听觉流，由多达12个单独的音轨组成。每个听觉动机都来自实际的RNA序列或元数据。这种方法已经被用来表示病毒RNA基因组的转录或翻译。该展示突出了功能RNA元件的实时相互作用。来自病毒RNA序列的所有三个阅读框架的密码子的发声与发声的元数据相结合，为这种展示提供了框架。功能RNA基序，如转录调节序列和茎环区域也被发声。使用该工具，可以从RNA的基因组或亚基因组表示中实时生成音频。考虑到病毒基因组的大小，已经提供了一组交互按钮来导航到感兴趣的区域，例如多蛋白中的切割区域、未翻译区域或每个基因。这些工具可以通过互联网浏览器获得，用户可以与数据显示实时交互。听觉展示与翻译和转录过程的实时动画相结合，为描述RNA基因组新陈代谢的大量证据提供了独特的见解。此外，该工具还被用作基于算法的音频生成器。这些音轨可以由普通社区收听，而无需参考视觉显示，以鼓励对科学的进一步研究。
This paper describes a web based tool that uses a combination of sonification and an animated display to inquire into the SARS-CoV-2 genome. The audio data is generated in real time from a variety of RNA motifs that are known to be important in the functioning of RNA. Additionally, metadata relating to RNA translation and transcription has been used to shape the auditory and visual displays. Together these tools provide a unique approach to further understand the metabolism of the viral RNA genome. This audio provides a further means to represent the function of the RNA in addition to traditional written and visual approaches. Sonification of the SARS-CoV-2 genomic RNA sequence results in a complex auditory stream composed of up to 12 individual audio tracks. Each auditory motive is derived from the actual RNA sequence or from metadata. This approach has been used to represent transcription or translation of the viral RNA genome. The display highlights the real-time interaction of functional RNA elements. The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. Functional RNA motifs such as transcription regulatory sequences and stem loop regions have also been sonified. Using the tool, audio can be generated in real-time from either genomic or sub-genomic representations of the RNA. Given the large size of the viral genome, a collection of interactive buttons has been provided to navigate to regions of interest, such as cleavage regions in the polyprotein, untranslated regions or each gene. These tools are available through an internet browser and the user can interact with the data display in real time. The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Furthermore, the tool has been used as an algorithmic based audio generator. These audio tracks can be listened to by the general community without reference to the visual display to encourage further inquiry into the science.
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