Symmetry observations in long nucleotide sequences

Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia

The relative quantities of bases in DNA were determined chemically many years before sequencing technologies permitted direct counting of bases. Apparently unaware of the rich literature on the topic, bioinformaticists are today rediscovering the 'wheels' of Chargaff, Wyatt and other biochemists. It follows from Chargaff's second parity rule (%A = %T, %G = %C for single stranded DNA) that the s...

New symmetry in nucleotide sequences

Information valuable words are the strings with the significant deviation of real frequency from the expected one. The expected frequency is determined through the maximum entropy principle of the reconstructed (extended) frequency dictionary of strings composed from the shorter words. The information valuable words are found to be the complementary palindromes: they are read equally in opposit...

Dyadic groups, dyadic trees and symmetries in long nucleotide sequences

The conception of multi-alphabetical genetics is considered. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have discovered algebraic properties of this system. These properties are connected with well-known notions of dyadic groups and dyadic-shift matrices. Matrix genetics shows relations of the genetic alphabets with some types of hypercomplex num...

Nucleotide sequences in DNA

Extendable words in nucleotide sequences

Previous statistical analyses revealed several peculiarities of nucleotide sequences that preclude their description by existing models and thus allow one to distinguish DNA and RNA sequences from random A,T,G,C-texts. This is a consequence of the unusual distribution of certain words in nucleotide sequences: while the distribution of (most) words is consistent with Markov models of small order...