Theta Palindromes in Theta Conjugates

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 generalization 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 $C_{\theta }(w)$.