Electrophoresis as physical data visualization.

The most easy, major way to visualize DNA is “gel electrophoresis”.  And it is one example of data visualization in physical fashion.

 

The left gel image, for example, shows the plots of DNA, with a scaled axis. This is a one dimensional chart.
Making of this picture is simple. after setting up agarose gel, mixtures containing several fragments of DNA are injected in the upper wells respectively; Then electronic voltage pull down DNAs –heavy (longer) one is remaining upper and light (shorter) one move further relatively. That’s one of the chromatography. But having the scale axis is a good feature (the ladder-like bands are DNA segments which length are pre-known so that we can use as a ruler).

So why I can say it is physical data visualization is its processing of DNA before electrophoresis, and the nature of DNA itself.
Typically, before injected wells on a gel, DNA is cut off and separated into some shorter fragments, by restriction enzyme. The enzyme plays the great role in searching for specific DNA sequence, then slicing DNA string on the location. By using it, we can discern different DNA or mutated DNA, comparing between the two lanes on the gel. Added, defective, or changed DNA sequence can be shown in differ band profiles.

What’s more; DNA has four kinds of base –ATGC. DNA sequences means word strings made of them.

 

So the whole process of DNA-electrophoresis is similar to usual ways of data visualization by programming: against a DNA sequence as a string, find matched word in it, slice it, and visualizing it based on these lengths — like a visualization of searching words.

Each step can be emulated in computer, so I am now making “electrophoresis image generator” for test driving of  D3.js as a visualizing tool. It’s half way now, but coming soon.

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