An auditory display tool for DNA sequence analysis

BMC Bioinformatics

Software

Mark D. Temple¹ 

[1] School of Science and Health, Western Sydney University, Campbelltown Campus, Locked Bag 1797, 1797, Penrith South DC, NSW, Australia;

关键词: Sonification;    DNA sequence;    Auditory display;   

DOI  :  10.1186/s12859-017-1632-x

 received in 2016-12-22, accepted in 2017-04-13,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundDNA 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.ResultsThe 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.ConclusionThis 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.

【 授权许可】

CC BY   
© The Author(s). 2017