Sonifying Protein Bio Synthesis (Version 7)
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*+ProteinBioSynthesis.zip+* (class library, distributed under *gpl*) !Sonification Library for Genetic Data "With the discovery that a set of symbols has been used by nature to encode the information for the construction and maintenance of all living things, semiotics - the analysis of languages and texts as sets of signs and symbols - has become relevant to molecular biology. Semiotics has given students of the DNA text a new eye for reading, allowing us to argue for the validity of a multiplicity of meanings, or even for the absence of any meaning, in a stretch of the human genome." (Pollack 1994: 12) *read an interview about biopiracy>http://www.inmotionmagazine.com/shiva.html* ProteinBioSynthesis (contains translation Dictionaries) AminoacidNames (converts from aminoacid index to name) GenomePattern (returns base letters) CodonPattern (returns triplets (codons)) AminoacidPattern2 (returns an array of index and codon) AminoacidPattern (returns aminoacid indices) Ptranscribe (return only the aminoacid indices between start- and stopcodon) AminoacidPattern3(returns an array of index and name) !sample genetic resources you can use to produce sound: *escherichia coli>http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi?val=AE005210* *Caenorhabditis elegans: Cruzia americana cytochrome oxidase subunit>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=9664175&dopt=GenBank* *Bacteriophage 3/14>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=951362&dopt=GenBank* *Orangutan hepadnavirus>http://www.ncbi.nlm.nih.gov:80/entrez/viewer.cgi?val=NC_002168* *Hepatitis B virus>http://www.ncbi.nlm.nih.gov:80/entrez/viewer.cgi?val=NC_001707* *a section of a y-chromosome>http://www.ncbi.nlm.nih.gov:80/entrez/viewer.cgi?val=NT_025347.1&from=1&to=39238&txt=on&view=gb* *Homo sapiens hypothetical protein MGC3200 (MGC3200), mRNA>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=14150063&dopt=GenBank* *Salmo salar ultraviolet opsin mRNA>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=14571554&dopt=GenBank* *Agrobacterium larrymoorei 16S rRNA>http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=773193&dopt=GenBank* ! acknowledgments Sophia Rohrhuber and Andreas Bartenstein helped with giving advice about the medical background to find more browse the *http://www.ncbi.nlm.nih.gov* search for genome and download the page. You can open any html page source code with the supercollider Genetics class GeneFile. If it is a larger file, it might take quite a while. Usually it takes a couple of seconds. (only lowercase base letters are supported at the moment) *Flicker Comparison of cDNA microarray images>http://www-lecb.ncifcrf.gov/mgapDB/* *Honiglab Imaging>http://honiglab.cpmc.columbia.edu/grasp/pictures.html* this program was developed during the *Telenautic Genome Project>http:/Institut/37* for viruses see also *Sammlung Rohrhuber>http://www.mikrokulturen.de/aasr_e.html* <p> What happens in a ribosome? In a process that is called transcription, specialized enzymes open up the bindings within the DNA doublehelix and produce a complementary copy of the base pattern that is called messenger RNA (mRNA). This single chain of nucleotides gets passed out of the core of the cell onto a structure called the epr (endoplasmatic riticulum) that acts like an intra-cellular transport system. On its surface there are large amounts of small round entities, the ribosomes, that translate the incoming mRNA into proteins. The ribosome always binds three nucleotides at a time and connects an aminoacid each to a growing chain. As aminoacids have various properties and shapes, this protein chain folds in a characteristic way that depends on complex factors and acts like a tool in the world of cellular chemical reactions. It must be mentioned that as a result of the everpresent brownian motion all molecules at this scale shake with an enourmous intensity - if they were more static, all those reactions couldn't happen. </p> These Patterns model the behaviour of ribosomes a close as meaningful. The sound is not mapped to individual nucleotides (the four letters), but to aminoacids. Aminoacids do not make sound really, so the mapping can be left to the musicians taste. Nevertheless, some mappings might be more meaningful than others. this topic is a classic one. one of the interesting links you may find is: *http://www.npr.org/programs/morning/features/2001/010212.cellsounds.html* a lego genome and other visualisations: *http://www.chemicalgraphics.com/paul/*
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