“Swine Flu Hemagglutinin”: amino acid sequence as ambient music

Swine flu has been sequenced.  More out of curiosity than anything else, I wrote code to translate a key gene into a piece of ambient music:

“Swine Flu Hemagglutinin” (MP3)

The algorithm I used is a bit complicated, but just in case you’re curious: since the gene is expressed as a surface protein antibodies can sense, it’s considered as a string of amino acids.  Each beat corresponds to one amino acid, and the piece is in 3/4 time, so each six measures would correspond to five turns around the alpha structure.  (I’m weaseling because I haven’t the foggiest idea how the protein actually gets folded.)  Amino acids with side chains that are neither aromatic not aliphatic control the piano and organ: the nine non-hydrophobics the piano, and the four hydrophobics the organ. The three amino acids with aliphatic side chains control the low synthesizer, while the four with aromatics control the percussion.  

ש

Update 2009-04-30: For folks coming in from the cnn.com article Making music out of swine flu and wondering about the line, “Zielinski saw it as a form of highly organized information that a human did not design.”: Yes, that phrasing raises the question of who or what I think DID design it. (God? Aliens?) In reality, self-organizing systems evince great complexity without need for a conscious designer. Swine flu was not designed at all– it evolved.

Strictly speaking, this is a version of swine flu hemagglutinin, FJ966952. The actual amino acid sequence:

MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE
QLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK
SYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ
EGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK
GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG
MVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR
IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS
LVLVVSLGAISFWMCSNGSLQCRICI

Maggie Koerth-Baker’s excellent article from 2009 April 28, “Swine Flu Q&A”, is available here:
Maggie Koerth-Baker, “Swine Flu Q&A”, at boingboing.net

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Posted Tuesday, April 28th, 2009 1:10 PM under . Comments and pings closed.
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