ALGORITHMIC COMBINATORICS ON PARTIAL WORDS

Abstract

Algorithmic combinatorics on partial words, or sequences of symbols over a finite alphabet that may have some do-not-know symbols or holes, has been developing in the past few years. Applications can be found, for instance, in molecular biology for the sequencing and analysis of DNA, in bio-inspired computing where partial words have been considered for identifying good encodings for DNA computations, and in data compression. In this paper, we focus on two areas of algorithmic combinatorics on partial words, namely, pattern avoidance and subword complexity. We discuss recent contributions as well as a number of open problems. In relation to pattern avoidance, we classify all binary patterns with respect to partial word avoidability, we classify all unary patterns with respect to hole sparsity, and we discuss avoiding abelian powers in partial words. In relation to subword complexity, we generate and count minimal Sturmian partial words, we construct de Bruijn partial words, and we construct partial words with subword complexities not achievable by full words (those without holes).