Visualize DNA sequence as a dot plot?

Question

[jaydu]

Hi!

Is there a very, very simple tool to visualize DNA in a dot plot or something like that?

I am basically looking to get an image where each base is represented by a 'dot' with a specific color, so red for A's, green for C's and so on. A single pixel dot might be to small to see, so maybe something like 4x4 pixels or maybe even the ability to set the size?

Thanks so much for your help!

[GenoMax]

Dot plot has a special meaning in bioinformatics. Are you simply looking for a linear representation of DNA as dots?

Answer 1

[Alex Reynolds]

You could use Python PIL (Pillow) to make one:

#!/usr/bin/env python

'''
pearl_plot.py
'''

import sys
from PIL import Image
from PIL import ImageDraw

# classic coloring scheme for DNA consensus sequence or logo
# ref. http://weblogo.threeplusone.com/manual.html 
#      https://github.com/WebLogo/weblogo/blob/master/weblogo/colorscheme.py
classic = {
    'G' : "orange",
    'T' : "red",
    'U' : "red",
    'C' : "blue",
    'A' : "green",
}

diameter = 20

for line in sys.stdin:
    line = line.rstrip().upper()
    img = Image.new("RGB", (diameter * len(line), diameter), color = "white")
    draw = ImageDraw.Draw(img)
    (x0, y0, x1, y1) = (0, 0, diameter, diameter)
    outline = "white"
    width = 1
    for char in line:
        bb = [x0, y0, x1, y1]
        fill = classic[char]
        draw.ellipse(bb, fill, outline, width)
        x0 += diameter
        x1 += diameter
    img.save("output.png")
    sys.exit(0)

Example:

$ echo "gaacgtacaacctatcaaataagggtcctctt" | ./pearl_plot.py
$ open output.png

To install Pillow:

• https://pillow.readthedocs.io/en/stable/installation.html

Dot plots have a different meaning to biologists. Consider a different name to avoid confusion.

Answer 2

[Alex Reynolds]

A text-based option might also be handy. Here's a Python script that uses the sty library:

#!/usr/bin/env python

'''
biostars9465050.py
'''

import sys
from sty import bg, rs

bg.orange = bg(202)

classic = {
    'G' : bg.orange,
    'T' : bg.red,
    'U' : bg.red,
    'C' : bg.blue,
    'A' : bg.green,
}

be = rs.bg

for line in sys.stdin:
    line = line.rstrip().upper()
    for char in line:
        if char in classic:
            sys.stdout.write(classic[char] + ' ' + be)
    sys.stdout.write('\n')

To install sty:

• https://sty.mewo.dev/intro/install.html

Example: