Reloaded genome visualization in 3D with OpenGL – formerly known as AGCT
2D DNA Walk
In conventional 2D DNA Walks a simple algorithm is used to draw a DNA walk by simply assigning a direction to each nucleotide such as T, C, A, and G correspond the East, South, West, and North directions in 2D, respectively. Reading the nucleotide sequence – nucleotide by nucleotide – following the rule – a path emerges like on the graph: Figure 1.
It is clearly shown that such a sequence of “ATATATATA” as an example would not lay a distinctive path in 2D, therefore the visualization might be misleading.
We need better solution.
3D DNA Walk
The 3D DNA walk sequence is not lossless either in its simplest implementation, but provides far more intuitive visualization in three dimensional space (3D), since it needs a long, distinctive sequence to intercept the path already drawn.
It is yet a simple algorithm to draw a DNA walk by assigning distinctive directions to each nucleotide such as T, C, A, and G correspond to four main directions, respectively in the three dimensional space (3D – following the diamond crystal structure as an example), and add colors for redundancy.
Reading the nucleotide sequence – nucleotide by nucleotide – following the new rule – a path emerges like on the graph: Figure 2.
Directions represent nucleotides as:
A - Up (towards Y axis)
G - Ahead down (towards X and down to -Y)
C - Aft down left (-Z, -Y)
T - Aft down right (+Z, -Y)
Bar colors represent nucleotides as:
A - Red
G - Yellow
C - Cyan
T - Green
Reference implementation of the 3D DNA Walk consists a computer software written in standard “C” programming language using OpenGL(R) based visualization for Windows(TM) and Linux operating systems.
The demo software can be downloaded from here freely for non commercial usage.
(Contact us for further conditions on commercial use.)
It demonstrates the visualization of eight DNA sequences as follows
(the number is passed to the software as command line argument):
case 1 - ALU - Human ALU interspersed repetitive sequence
case 2 - MLT1 - Interspersed repeat MLT1- a consensus
case 3 - L1 - Human L1 interspersed repetitive sequence - full length copy
case 4 - Tigger1 - Autonomous DNA transposon
case 5 - Tigger2 - Autonomous DNA transposon
case 6 - TAR1 - Human telomere associated repeat sequence, complete sequence
case 7 – SemaphorinE - membrane proteins, a.k.a. M0195 TRANSCRIPT or EXON 1 524 bp.
case 8 – GPI_Anchored – Chromosome Number 08 - ef NT_000511 Hs8_1001 Homo sapiens
(Music by Julia A. Miller (c) FMA)