An auditory display tool for DNA sequence analysis
An auditory display tool for DNA sequence analysis
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DOI：
10.1186/s12859-017-1632-x
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发表时间：
2017-04-24
影响因子：
3
通讯作者：
Temple, Mark D.
中科院分区：
文献类型：
--
作者：
Temple, Mark D.
背景：DNA 听觉化是指利用听觉显示来传达 DNA 序列数据的信息内容。提出了六种可听化算法，每种算法都会产生听觉显示。这些算法的逻辑设计从简单到复杂。其中三个将单个核苷酸、核苷酸对或密码子解析为音符，分别产生 4、16 或 64 个音符。密码子也可以被简并解析为关于遗传密码的 20 个注释。最后，核苷酸对可以被解析为两个单独的框架，或者密码子可以被解析为三个阅读框架，从而产生多个音频流。结果：信息最丰富的声音化算法将 DNA 序列读取为三个阅读框架中的密码子，从而在听觉显示中产生三个并发的音频流。这种方法是有利的，因为任一帧中的起始密码子和终止密码子对该帧中的音频的启动或停止具有直接影响，而其他帧不受影响。使用这些方法，可以将诸如开放阅读框或重复DNA序列之类的DNA序列彼此区分开。这些声音化工具可通过网页界面使用，其中可以实时处理输入的 DNA 序列，以产生可直接在浏览器中播放的听觉显示。参考来自测试序列（包括简单核苷酸序列、重复 DNA 序列和编码或非编码基因）的听觉显示，讨论了这种方法作为分析工具的潜力。结论：这项研究提出了一个概念验证，即 DNA 序列的某些属性可以仅通过声音化来识别，并主张将它们包含在 DNA 序列浏览器工具包中，作为现有视觉和分析工具的辅助。
Background: DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code. Lastly nucleotide pairs can be parsed as two separate frames or codons can be parsed as three reading frames giving rise to multiple streams of audio.Results: The most informative sonification algorithm reads the DNA sequence as codons in three reading frames to produce three concurrent streams of audio in an auditory display. This approach is advantageous since start and stop codons in either frame have a direct affect to start or stop the audio in that frame, leaving the other frames unaffected. Using these methods, DNA sequences such as open reading frames or repetitive DNA sequences can be distinguished from one another. These sonification tools are available through a webpage interface in which an input DNA sequence can be processed in real time to produce an auditory display playable directly within the browser. The potential of this approach as an analytical tool is discussed with reference to auditory displays derived from test sequences including simple nucleotide sequences, repetitive DNA sequences and coding or non-coding genes.Conclusion: This study presents a proof-of-concept that some properties of a DNA sequence can be identified through sonification alone and argues for their inclusion within the toolkit of DNA sequence browsers as an adjunct to existing visual and analytical tools.