Practical variable length gap pattern matching

Abstract

Solving the problem of reporting all occurrences of patterns containing variable length gaps in an input text T efficiently is important for various applications in a broad range of domains such as Bioinformatics or Natural Language Processing. In this paper we present an efficient solution for static inputs which utilizes the wavelet tree of the suffix array. The algorithm partially traverses the wavelet tree to find matches and can be easily adapted to several variants of the problem. We explore the practical properties of our solution in an experimental study where we compare to online and semi-indexed solutions using standard datasets. The experiments show that our approach is the best choice for searching patterns with many gaps in large texts.