Theta palindromes in theta conjugates

TL;DR

This paper explores the distribution and properties of theta-palindromes and theta-conjugates in DNA sequences, extending classical concepts of palindromes with Watson-Crick involution, and characterizes words with maximal theta-conjugate sets.

Contribution

It introduces the concept of theta-conjugates in relation to Watson-Crick palindromes and characterizes words with maximum theta-conjugate elements and those containing WK-palindromes.

Findings

Characterization of words with maximum theta-conjugates

Distribution patterns of theta-palindromes among conjugates

Structural analysis of words containing WK-palindromes

Abstract

A DNA string is a Watson-Crick (WK) palindrome when the complement of its reverse is equal to itself. The Watson-Crick mapping $\theta$ is an involution that is also an antimorphism. $\theta$-conjugates of a word is a generalisation of conjugates of a word that incorporates the notion of WK-involution $\theta$. In this paper, we study the distribution of palindromes and Watson-Crick palindromes, also known as $\theta$-palindromes among both the set of conjugates and $\theta$-conjugates of a word $w$. We also consider some general properties of the set $C_{\theta}(w)$, i.e., the set of $\theta$-conjugates of a word $w$, and characterize words $w$ such that $|C_{\theta}(w)|=|w|+1$, i.e., with the maximum number of elements in $C_{\theta}(w)$. We also find the structure of words that have at least one (WK)-palindrome in $C_{\theta}(w)$.