Gates MA. A simple way to look at DNA. J Theor Biol. 1986;119(3):319-328. doi:10.1016/s0022-5193(86)80144-8

Example Usage

gates('ATGC')
// returns [[0, 0, 0, 1, 0], [0, -1, 0, 0, 0]]

In Gates’s method, DNA sequences are converted into 2D walks in which Ts, As, Cs, and Gs are up, down, left, and right, respectively. This gives each sequence a “shape.” However, there is degeneracy, meaning that a visualization is not necessarily unique. For example, TGAC is a square (up, right, down, and left), but so is GTCA (right, up, left, down).

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#gates

Qi, Z., & Qi, X. (2007). Novel 2D graphical representation of DNA sequence based on dual nucleotides. Chemical Physics Letters, 440(1–3), 139–144. doi:10.1016/j.cplett.2007.03.107.

Example Usage

qi('ATGC')
// returns [[0, 1, 2], [8, 7, 11]]

Similar to Randic, Qi maps each 2-mer in the sequence to a unique y-value. Because there are more 2-mer combinations than lone bases, Qi graphs look like randic graphs with a larger range of y-values.

Qi Assignment Key:

AA = 12
AC = 4
GT = 6
AG = 0
CC = 13
CA = 5
CG = 10
TT = 15
GG = 14
GC = 11
AT = 8
GA = 1
TG = 7
TA = 9
TC = 3
CT = 2

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#randic-and-qi

Randić, M., Vračko, M., Lerš, N., & Plavšić, D. (2003). Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chemical Physics Letters, 368(1–2), 1–6. doi:10.1016/s0009-2614(02)01784-0.

Example Usage

randic('ATGC')
// returns [[0, 1, 2, 3], [3, 2, 1, 0]]

Similar to tabalture, the Randic method assigns each base a different y-value.

Specifically:

A = 3
T = 2
G = 1
C = 0

*This visualization method isn't well suited to long sequences

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#randic-and-qi

Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. Bioinformatics. doi:10.1093/bioinformatics/bty807.

Example Usage

squiggle('ATGC')
// returns [[0, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4], [0, 0.5, 0, -0.5, -1, -0.5, 0, -0.5, 0]]

Squiggle’s DNA visualization method is based on the UCSC .2bit format and the Qi et. al Huffman coding method. In essence, a DNA sequence is first converted into binary using the 2bit encoding scheme that maps T to 00, C to 01, A to 10, and G to 11. The bits can be mapped as end to end vectors.

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#squiggle

Yau, S. S., Wang, J., Niknejad, A., Lu, C., Jin, N., & Ho, Y. K. (2003). DNA sequence representation without degeneracy. Nucleic acids research, 31(12), 3078-80.

Example Usage

yau('ATGC')
// returns [[0, 0.5, 1, 1 + 3 ** 0.5 / 2, 1 + 2 * (3 ** 0.5 / 2)], [0, -(3 ** 0.5 / 2), 0, -0.5, 0]]

Yau et. al’s method uses unit vectors with upward vectors indicating pyrimidine bases (C and T) and downward vectors indicating purine bases (A and G). Similar to Squiggle, this method has no degeneracy.

The unit vectors are based on 30 and 60 degree values on the unit circle.

Specifically:

A = (0.5, -3**0.5/2) // ** represents exponents in js
T = (0.5, 3**0.5/2)
C = (3**0.5/2, 0.5)
G = (3**0.5/2, -0.5)

*Warning: The x-coordinate is not equivalent to the base position

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#yau

Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. Bioinformatics*. doi:10.1093/bioinformatics/bty807. Yau, S. S., Wang, J., Niknejad, A., Lu, C., Jin, N., & Ho, Y. K. (2003). DNA sequence representation without degeneracy. *Nucleic acids research, 31(12), 3078-80.

Example Usage

yau_bp('ATGC')
// returns [[0, 1, 2, 3, 4], [0, -1, 0, -0.5, 0]]

Unique to DNAViz is the Yau-BP method, a slight modification of Yau’s method that ensures that the x axis is equivalent to the base position. It preserves that salient feature of the method, which is the purine/pyrimidine split.

For more information visit: https://squiggle.readthedocs.io/en/latest/methods.html#yau-bp