Quantifying Local Randomness in Human DNA and RNA Sequences Using Erdos Motifs

TL;DR

This study investigates the local randomness of human DNA and RNA sequences by analyzing Erdos motifs, revealing distinct patterns of under- and overrepresentation related to nucleotide properties.

Contribution

It introduces a novel application of Erdos motifs to quantify local randomness in biological sequences, linking mathematical concepts with genomic data analysis.

Findings

Purine/pyrimidine Erdos motifs are underrepresented in human DNA.

Strong/weak base pair Erdos motifs are slightly overrepresented.

Erdos motif densities are negatively correlated in DNA sequences.

Abstract

In 1932, Paul Erdos asked whether a random walk constructed from a binary sequence can achieve the lowest possible deviation (lowest discrepancy), for the sequence itself and for all its subsequences formed by homogeneous arithmetic progressions. Although avoiding low discrepancy is impossible for infinite sequences, as recently proven by Terence Tao, attempts were made to construct such sequences with finite lengths. We recognize that such constructed sequences (we call these "Erdos sequences") exhibit certain hallmarks of randomness at the local level: they show roughly equal frequencies of subsequences, and at the same time exclude the trivial periodic patterns. For the human DNA we examine the frequency of a set of Erdos motifs of length-10 using three nucleotides-to-binary mappings. The particular length-10 Erdos sequence is derived by the length-11 Mathias sequence and is identical with the first 10 digits of the Thue-Morse sequence, underscoring the fact that both are deficient in periodicities. Our calculations indicate that: (1) the purine (A and G)/pyridimine (C and T) based Erdos motifs are greatly underrepresented in the human genome, (2) the strong(G and C)/weak(A and T) based Erdos motifs are slightly overrepresented, (3) the densities of the two are negatively correlated, (4) the Erdos motifs based on all three mappings being combined are slightly underrepresented, and (5) the strong/weak based Erdos motifs are greatly overrepresented in the human messenger RNA sequences.