Visual Properties of E.Coli K-12 MG1655

 

01. E.coliK-12

A couple of years ago I was suggested to try implementing my method of RNA and DNA visualization based on five shades of gray (from black to white) and a 2D matrix 3×4, on the E.coli K-12 MG1655 bacteria strand. I accepted the suggestion and spent one entire summer extracting from this strand of 4639675 positions all the binary stretches consisting only of A and T that are 12 positions long.

02 E.coliK-12

I was particularly interested in those stretches that are either highly organized(low entropy) or that have low organization(high entropy). Highly organized states are with minimal number of neighborhoods between different elements(J-junctions), in this case A and T, or maximal number of neighborhoods between the same elements (C-connections), A and A or T and T.

3aa

In case of 3×4 matrix and binary stretches with equal number of both bases(6A +6T) there are 8 types   of highly organized states and only one with the lowest organization(chessboard). Among those highly organized I found only one stretch of 12 positions that has the highest organization AAAAAATTTTTT and no one case of a stretch with the lowest organization ATATATATATAT.

04 E.coliK-12

Later I sent these results to Victor Norris, who suggested this research, and to Dave Ussery:

Dear Dave and Vic,

Yesterday I finished my three months long expedition through this E.coli strand of 4639675 positions and I manage to find 4456 stretches consisting only of A and T that are 12 positions long. Almost exactly 0.1% of the entire strand. I do not expect that I missed more than 5%. It will take some time now to analyze and sort out all the results, but I was already able to identify those states which I call highly organized. There are 8 types of these kind of states and they come in some variations. Altogether I found only 40 of them as you could see in the attachment.

05. E.coliK-12

 

06. E.coliK-12

On the other hand I didn’t find any stretch that corresponds to the state with the lowest organization (highest  entropy): TATATATATATA or ATATATATATAT, but I noticed some that are just “one step away”. I also  didn’t find any 12 positions long stretch TTTTTTTTTTTT or AAAAAAAAAAAA.  However, I noticed a few cases with 11:1 ratio.

Best, Greg

 

And in another mail to Jon Bohlin:

…After going through the E.coli strand I realized that there are specific rules how these images are generated I wasn’t aware of before. In the attachment is the first AT stretch I encountered. It is 17 bases long, begins with position 96 and ends at 112. The first 12 bases generate the first image (96-107). Now, when we move the “frame” one position to the right we will get the second image (97-108). If we pay attention to the vertical “lines”, there are three of them. We’ll mark the first vertical to the left with (I), the middle with (II) and the last on the right with (III). 

10 E.coliK-12

If each particular state(frame) is interpreted as “now”, then those verticals are the thee segments of “now”:  (I) being the “past”, (II) the “present” and (III) the “future”.

09 E.coliK-12

 

Gregor Mobius,

Summer 2012

http://www.visualdna.org

https://www.youtube.com/results?search_query=DNA+Semantics

gregor.mobius@jps.net

 

 

 

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