The geometry of DNA by Ivan Stepanyan and Sergey Petoukhov

Information journal delighted to see it has raised a lot of interest since  publication “The Matrix Method of Representation, Analysis and Classification of  Long Genetic Sequences” at: http://www.mdpi.com/2078-2489/8/1/12 by Ivan V. Stepanyan  and Sergey V. Petoukhov from Mechanical Engineering Research Institute of the Russian Academy of Sciences, Moscow, Russia.

The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed.

The geometry representations of DNA of some different organisms:

Examples of visual patterns, which have been received on the base of the described method for different nucleotide sequences (see explanation in the text of full article). Two symbols are shown at the right side of each pattern to indicate what kinds of the sub-alphabets were used to construct the pattern.

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