Exploratory Genomics with Clojure

John Jacobsen
Friday, July 5, 2013

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Earlier post Rosalind Problems in Clojure code clojure

Later post A Two Bit Decoder code clojure

In Stanislaw Lem’s His Master’s Voice, humanity receives a “letter from the stars,” in the form of regularly repeating binary data encoded in a beam of extraterrestrial neutrinos. The protagonists know nothing a priori about the content of the letter. The plot unfolds as the message slowly, as a result of careful study, yields a few (not many) of the signal’s secrets.

What would you do if you received such a dataset? How would you study it? What real world datasets are similarly mysterious?

As most readers will know, every living being contains a “message” of sorts, encoded, not in base 2 (binary), but rather base 4: A, G, C, or T, arranged in paired, sequential molecular strands called DNA (in which every A is paired with a T, every C with a G). From 159,662 base pairs for the smallest known genome, to 3.3 billion BPs for humans, to 149 billion BPs for the largest genome, that of Paris japonica, each organism carries its own unique tome locked in its cells.

In the past ten years, the human genome has been sequenced and made widely available. Though downloadable in a variety of formats, the most compact seems to be the ‘2bit’ format (two bits per base pair): the genome in this format is just under a gigabyte, uncompressed. Plenty of genomes of simpler organisms are available for study as well.

I am not a genomicist or biologist, but am curious about the properties of the “data” stored within us all. In the next few blog posts I intend to investigate genomic data (human or otherwise) using Clojure, a modern Lisp developed for the JVM. Clojure’s strengths are simplicity, concurrency, expressiveness and speed – assets which will be helpful as we tackle a few simple analytical tasks aimed at understanding some of the properties of life’s very own “Big Data.”

Next: A Two Bit Decoder.

Earlier post Rosalind Problems in Clojure code clojure

Later post A Two Bit Decoder code clojure

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Reflections on a Year of Daily Memory Drawings art

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Getting Our Hands Dirty (with the Human Genome) code clojure

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A Two Bit Decoder code clojure

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