Walking on nucleotides

ARAGÓN ARTACHO, Francisco J., et al.[1] presents new ways to visualize large mathematical datasets. In particular, the paper goes into determining if a real number is "Normal" through visualizations.

”A real constant α is b-normal if, given the positive integer b ≥ 2, every m-long string of base-b digits appears in the base-b expansion of α with precisely the expected limiting frequency 1/bm."

The paper shows a visualization of many base 4 numbers. The authors also go on to suggest applying this visualization technique to genome comparisons.

[1] ARAGÓN ARTACHO, Francisco J., et al. "Walking on real numbers". The Mathematical Intelligencer. Vol. 35, Issue 1 (March 2013). ISSN 0343-6993, pp. 42-60

Visualization

A walk for a base 4 number consists of steps where at each step the path moves one unit east, north, west or south, depending on the whether the
number at that position is 0, 1, 2 or 3.

I've applied this visualization technique to DNA. DNA consists of 4 nucleotides denoted by A, T, G and C. For each of these nucleotides, I assigned a direction to the step - North, East, South, and West respectively.

Instead of the HSV color scheme used in the paper, that generates a spectrum of colors from VIBGYOR, I've used fixed colors for each nucleotide to get an idea of the nucleotide content in the sequence which is of value in sequence analysis.

Color Scheme

  • A - #D9042B
  • T - #03588C
  • G - #F29F05
  • C - #F24B0F

I picked up the color scheme from Adobe Color.

Data Sources

Thanks to

All the folks at the Andersen Lab.

For More Data ...

At the Andersen Lab we are sequencing Zika virus in samples from humans and mosquitoes in Florida, USA. We're regularly releasing data available here.

Code at Github

Nucleotide Walk Potraits


I've uploaded all the images shown below here.

Fig 1 shows strains of Zika virus from humans and mosquitoes in Florida, USA sequenced at the Andersen Lab. Fig 2 shows a few flaviruses - Chaoyang Virus, Culiseta Virus, Powassan Virus and West Nile Virus. Notice how both the figures capture the difference in mutations.

Zika strains Fig 1: Strains of Zika virus from GenBank.

Clockwise:

Fig 2: A few Flaviviruses from GenBank

Clockwise:

Human chromosome walks

Images of human chromosomes show very similar A,T,G and C content(except for Chr22 and Chr19). I'm looking into producing gigapixel images to allow zooming to make the walks clearer.

Disclaimer: I'm quite busy with my work at the lab so it will be a while before I can get around to doing it.

Chr 22 Fig3a: Chromosome 22 Chr 21 Fig3b: Chromosome 21 Chr 20 Fig3c: Chromosome 20 Chr 19 Fig3d: Chromosome 19 Chr 18 Fig3e: Chromosome 18 Fig3f: Chromosome 17 Fig3g: Chromosome 16 Fig3h: Chromosome 15 Fig3i: Chromosome 14 Fig3j: Chromosome 13 Fig3k: Chromosome 12 Fig3l: Chromosome 11 Fig3m: Chromosome 10 Fig3n: Chromosome 9 Fig3o: Chromosome 8 Fig3p: Chromosome 7 Fig3q: Chromosome 6 Fig3r: Chromosome 5 Fig3s: Chromosome 4 Fig3t: Chromosome 3 Fig3u: Chromosome 2 Fig3v: Chromosome 1 Fig3w: Chromosome X Fig3x: Chromosome Y

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