5/20/2023 0 Comments Sequence analysisTo date, auditory displays have not been widely accepted as a complement to standard visualization of DNA sequence data and they are typically considered to be an interesting oddity that contributes little analytical benefit. Presented herein is one further option to enhance DNA sequence analyses through DNA sonification to create a supplementary auditory display within the browser. During the past decade there has been a phenomenal increase in the accumulation and storage of DNA sequence data and the strong demand to interrogate these data has lead to the development of many high quality and freely available tools within genomic browsers. Additionally, the occurrence of start or stop codons in either reading frame can be used to turn an audio stream on or off, respectively, which allude to the way DNA may be processed within the cell.ĭNA sequence data is linear information that is highly amenable to being sonified within a genomic browser to produce audio. These can be used to distinguish complex DNA sequence data from repetitive data. For example, DNA motifs from each of three reading frames may each be assigned to a unique sound to produce three concurrent streams of audio. These algorithms use codons to generate strings of audio that are representative of ribonucleotides synthesised during transcription. This paper demonstrated that sonification of DNA sequence data, using algorithms based on biological rules, is useful to determining its properties. Today's computers are highly capable of performing a variety of analytical tasks to identify otherwise hidden patterns in complex data, one such application has been in the field of genomic data analyses. This is an early example of computerised sonification to track the real time progress of a complex routine over an extended period of time. The Programmers’ Handbook for this computer states that “some indication of what is going on is given by the rhythm of the clicks that are heard’. 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.Īlan Turing’s Manchester computer build in 1948 had a built in loudspeaker (referred to as a hooter) that could generate taps, clicks and thumps to indicate the progress of programmed routines. 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. 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. Using these methods, DNA sequences such as open reading frames or repetitive DNA sequences can be distinguished from one another. 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. 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. 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. Codons may also be parsed degenerately into 20 notes with respect to the genetic code. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. These algorithms are logically designed from the simple through to the more complex. Six sonification algorithms are presented that each produce an auditory display. DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data.
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