Edit: Feel free to edit this page if you're interested in working on a project like this.
I am interested in turning protein sequences into some form of audio. The basic concept is to turn the 20 or so different amino acids in the protein sequence (which can range from 50 to 100s of amino acids long) into some kind of audio signal, and then analyze the signal.
I mainly work in bioinformatics, so I'm not very knowledgeable on the audio processing end, but I have access to a lot of different protein sequences to work with. I'm open to suggestions and really any ideas related to biology or bioinformatics in general.
Hey Tim, hope it's ok if I edit this, I didn't know if my project ideas would warrant a new link… I was also thinking of some sort of genome to audio translation. On a massive scale, wouldn't it be beautiful to input your DNA, and output a symphony? Obviously that's unachievably huge right now, and we're not about to go sequencing our own genomes, but there are a number of fully sequenced bacteria/plants/animals that we could use to produce something along the lines of… riffs on Haemophilus influenzae, for example.
Similarly, I was also thinking it would be really neat to create a demographic/epidemiologic data –> audio program that would basically take an equation as input (I guess the program would solve a linear or logistic regression of user-input variables on perhaps age [continuous], gender [binary], race [categorical], other variables of interest) - could be cool to create sound profiles of individuals or risk groups for various diseases? I haven't entirely hammered out this thought.
Hey there, a quick suggestion… You probably don't want to start synthesizing audio from scratch, as there are tons of synthesis engines out there. I have used ChucK recently for a sonification project. A more popular audio synthesis environment/engine is SuperCollider. There might be a learning curve to figuring out the programming syntax for these synthesis engines. But if you get past that (or solicit someone who already knows), you can probably create lots of fun mappings between bioinformatic data and audio.
Eli: Both those ideas sound really cool. The first idea I was thinking we could either convert protein or genomic sequence into a riff, or perhaps into one sound, using various frequencies for amino acids. I'm not really sure how well either of them would go, how feasible it is, and whether it'd even sound remotely interesting! But I'm open minded. As for your second idea, do you have a dataset to work with? I'm not really sure how we'd sonify the data, but it's definitely along the lines of something I'd be interested in doing.
Andy: I appreciate the tip. I downloaded both those programs, so at the very least, I'll be able to take a look at them this weekend.
If there's anyone else interested in a project like this, feel free to edit this post with your comments!
Audio representation of a protein sequence
A protein is comprised of a sequence of amino acids. Each amino acid may be represented by an SLC, so a protein sequence may be input as a string like this:
Amino acids are encoded by 3-base DNA codons. There are four bases: A, T, C, and G. Therefore, there are 4*4*4=64 possible 3-base codons. A protein sequence may therefore also be represented by a string of bases.
There are 20 naturally-occuring amino acids, but all possible codons encode for an amino acid (with three “stop” codons), which means that there is redundancy. For example, there are three codons for isoleucine: ATT, ATC, and ATA. Therefore, the same sequence may be represented by a different string of base pairs, that however corresponds to the same string of amino acids (and therefore the same protein).
The question is, how do we translate a sequence into some sort of audio output? Let's try to start with some trivial exercises, and work up to more complex (and hopefully meaningful/interesting/musical) audio representations.
Amino acid classes –> timbres, and each AA within a class is a different pitch
Side-chain polarity –> rhythmic gating
Side-chain charge –> panning
*H is neutral 90% of the time, positive 10% of the time
Hydropathy index –> amplitude (neg –> pos) R, K, D, E, N, Q, H, P, Y, W, S, T, G, A, M, C, F, L, V, I
Hemoglobin subunit alpha (Homo sapiens):
Hemoglobin subunit beta (Homo sapiens):
RuBisCO small subunit (Plocamium serrulatum): mritqgtfsflpdltdeqikkqveyaiskkwsvgieytedphprnsywel
RuBisCO large subunit (Plocamium serrulatum):
P53 wild type (Homo sapiens):
P53 isoform b (Homo sapiens):
P53 isoform c (Homo sapiens):
Insulin (Homo sapiens):
Insulin (Octodon degus):
Insulin (Ovis aries):
Insulin (Oryctolagus cuniculus):