{"id":14359,"date":"2017-07-17T16:00:12","date_gmt":"2017-07-17T15:00:12","guid":{"rendered":"https:\/\/blogs.nature.com\/naturejobs\/?p=14359"},"modified":"2017-07-26T21:14:14","modified_gmt":"2017-07-26T20:14:14","slug":"the-sound-of-dna","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/naturejobs\/2017\/07\/17\/the-sound-of-dna\/","title":{"rendered":"TechBlog: The sound of DNA"},"content":{"rendered":"
\"DNA<\/a>

{credit}Mark Temple{\/credit}<\/p><\/div>\n

With an alphabet comprising just four letters, DNA sequence isn\u2019t much to look at. So, when sequence analysis tools\u00a0want to highlight key elements, they typically do so using colour, font, or by overlaying other types of information. In the not-too-distant future, there may be another option: Audio.<\/p>\n

In a paper published this past April in BMC Bioinformatics<\/a><\/em>, molecular biologist and part-time drummer Mark Temple<\/a> of Western Sydney University, Australia, describes \u201can auditory display tool\u201d for DNA: sequence in, audio out.<\/p>\n

Available online at dnasonification.org<\/a>, the tool does precisely what it sounds like: Given a sequence of DNA, it will convert the As, Cs, Gs, and Ts into notes played by a virtual piano, guitar, and organ. An ancillary browser extension, called Jazz-Plugin, is required to play the resulting MIDI files, though Temple has made a number of example MP3\u00a0files available on his web site and\u00a0on YouTube<\/a>.<\/p>\n

After uploading a sequence, the user can select precisely how the musical transcription is accomplished. The simplest mode maps each base to a single note, providing a four-tone auditory landscape. Another maps dinucleotides to notes, increasing the complexity to 16 total sounds.<\/p>\n

Most informative, says Temple, is the trinucleotide mode. Here, the software maps each nucleotide triplet to one of 20 notes, and outputs the audio in each of three reading frames at once, just as the genetic code maps 64 codons to 20 amino acids. The result is a series of three-note arpeggios \u2013 CGF-ADD-CFF-DFG-AFC-GCD-FCD-FCD, for instance. Optional parameters allow the user to flag start and stop codons, or to cause audio in each reading frame to turn on and off as start and stop codons arise.<\/p>\n

Genome browsers, Temple explains, typically use visual cues to make key sequences stand out; audio, he figured, could provide a useful accompaniment. \u201cI\u2019m not saying audio by itself is the bees\u2019 knees<\/a> for interpreting DNA sequence,\u201d he says, \u201cbut surely audio can contribute to your visual interpretation.\u201d<\/p>\n

That\u2019s particularly true for repetitive elements, slight alterations in which can be difficult to pick out by eye. In one example, Temple provides a\u00a0sequence of\u00a0human telomeres \u2013 the highly repetitive sequences found at the end of eukaryotic chromosomes. The \u201csonified\u201d sequence sounds unremarkable and repetitive until it reaches a single base insertion, at which point\u00a0the music shifts, as if the musician was inspired to shake things up. (Check out an MP3 of the\u00a0audio here<\/a>, and a video below)<\/p>\n