A couple of years ago Prof. David Ussery suggested I could try this my method for visually representing DNA/RNA on the Mumps RNA. Some of the results, ending with position p.192, are already published on the ArC-GEM and rest of the results, ending with position p.3072, are now presented here.
This particular visualization of Mumps RNA is based on the idea that all RNA/DNA basis could be represented as five discrete values of the gray-scale: U=black(100%), C=dark(75%), A=gray(50%), G=light(25%) and T=white(0%), while the linear RNA structure could be converted into 2D images built of 3×4 basic matrices(fig.1). In this representation the value difference between neighboring bases is 25% and between the base-pairs it is 50%.
This paper shows how this algorithm is implemented on the first 3072 positions of the Mumps RNA, both as a set of individual 3×4 matrices(micro-visualization) and as one integrated image (macro-visualization). In principle there are two ways to organize (linear)stretches in 3×4 matrices(2D images). After an image of a stretch is generated with its first 12 positions, starting, let’s say, with position p.1, then there are two options for the next image. In one, the second image would start with the positions p.2, third with position p.3, fourth with p.4,.. etc. (Fig.2).
In another option the second image starts with p.13, the third with p.25, then comes p.37… etc. (Fig.3). In the first option, from positions p.1 to p.25 there are 14 images, and
this approach resembles recording with a movie camera. As if some special camera with a frame that covers 12 positions at the time and converts them in 2D images is moving through a DNA/RNA stretch, one base at the time. In another option from position p.1 to p.25 there are only two images. In this case it resembles taking a snapshot after moving 12 positions from a previous image. The first algorithm, one that resembles film strip, we will mark with F, while the second, that is a snapshot like, we will mark with S. In a way, the algorithm F could be interpreted as being time based, while S would be timeless. A set of images generating from a stretch of DNA/RNA with algorithm S is a subset of a set generated from the same stretch with algorithm F.It is this second algorithm(S) that is implemented in the Mumps RNA stretches presented here since this way generated images can be grouped in larger images. It seems that images generated by F could be presented only as a series of successive micro states, as a film strip that could be even projected as an animated film.
A few examples of mostly binary stretches represented through algorithm F, as a film strips, are shown on the last page of the paper.
Gregor Mobius New York, October 2018
This is integrated image from position p.1 to position p. 1536
This is integrated image from position p.1537 to position p. 3072.
And these are integrated images from position p.1 to position p. 3072
At the end, a few interesting, mostly binary, stretches generated with algorithm F.