Method for identification of new generated transposable elements.
Publication Date: 2016-Jul-01
The IP.com Prior Art Database
Identification of new born copy of Transposable Elements in complex organism is problematic.
In order to identify new TE in Mammal the following approach should be taken
Use a Cow as the tested organism The reason for choosing a cow, is due to the fact this mammal has a very high copies Number of TE mostly originated in Squamata. And found only in Ruminatia and Mostly Snakes
The selected COW must be of type Solid Red With the standard genetics of Homozygous Recessive Red on the Extension (MC1R) and Non Agouti (Solid) This is regular recessive solid red-cow
This Organism ensure that in case a Genetic Mutation will affect the Extension Gene or the Agouti gene We will likely to see a difference in hair color using the naked eye
Since the Recessive Red requires both copy to hold Red This ensure that in case of a New Transposable Element copied into one of the 2 main color genes the result will be a modified Hair Color into Black or White.
Since the Chances for the 2 DNA Strands to get hit with TE in the same location are close to 0 We must use a recessive color system to ensure even one strand modification will modify the gene expression.
This basically turn the solid red cow hair into a high resolution monitor for identification of new transposons.
As for the Cow, once the cow starts to grow Look for newly born Black or White Her, Preferred to look for group of at least 2 or more black/white hers that are located next to each other. Those will likely to appear already in young age at very small quantities As a general rule the majority of the red cows in the world will have many location containing 2 or more black hers, hidden inside the Red Hair. They might even grow into larger spotting. Pull those modified hair from the root and analyze the 2 Gene Locations. (Agouti and the Extension) Or any new gene that had being discovered to effect hair color. My prediction will be that you will find a newly transmitted TE copied into one of those genes and crippling the Gene expression. Since most of the Cow and Ruminatia TE are originated from Squamata, my prediction will be that the new copy of TE will be a result of this group as well.
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Working Station - a Genome Visualizer Environment
As a starting point, my Working Station changes the genome representation into a 2 dimensional picture. The station changes any letter in the genome, to 1 of 4 pixel colors. Proper selection of colors, creates good contrast, and the coding regions are usually exposed in the picture as regions with more cyan and purple colors. The non-coding regions will usually present Yellow and Red tones regions.
The Station works only in 4K resolution of 3840 * 2160 totaling over 8 million pixels per page.
This means all human genome will be graphically represented as close to 400, 4K pages.
The Station always holds one genome picture and one masking picture in memory, and lets you swap in a click between the genome picture, and the mask.
The masking is determined by the function you want to apply on any particular genome page.
You can scroll up and down any standard genome FASTA file in rendering speed of 1 second per page. This allows me to expose to the eye all the human genome in about 7 minutes. Practically all the pixels in the genome are presented to the viewer.
On each page, you can move with the mouse around the picture zooming down to a resolution of actual readable code.
The unit is hooked into a set of proprietary SQL server based blasters, which can activate different functions as required. The rendering speed depends on the complexity of the function, at the moment all of the functions are designed with Multithread approach and in each single rendering many workers are working at the same time to each handle a different part of the bitmap.
Currently those are rendered using 48 cores in parallel and then composed to one picture by single thread. I found it very practical to run a quick test on one or two pages as start, and then see if it's worth it to leave it for few hours, doing a full genome frame set of that particular function.
Then, once a completed set is made and saved, you can now join the new analysis to the rendering system keeping it in 1 sec per render speed, (and maybe mask another layer of another function on those).
Example 1: Repeat Mask
I have attached an example (2 pictures) showing how a repeat mask function will render the mask of a human particular page. I intentionally picked up a picture with very high repetitive pattern.
And also one that has a visible strange arrangement pattern. (Would appreciate any feedback what are those, I am aware that the cost to compose these are extensive).
One of those patterns appear on each chromosome, in sizes of about 3-5 Mega letters.
They are all different but all from the same family of pattern, and uses different building blocks in different chromosomes.
Note: 2 Pictures. HUMAN_GENOME_p110.JPG and HUMAN_RMASK_P110.jpg
Shared Links: https://drive.google.com/file/d/0B2PzQd2QkAEleW5MNDBMVDlYM28/view?usp=sharing
The repeat mask picture paint each p...