Pattern Kits

TL;DR

This paper introduces a space- and time-efficient data structure for managing a dynamic library of patterns in self-indexes, enabling efficient concatenation searches and pattern manipulations.

Contribution

It presents a novel data structure that efficiently supports pattern concatenation and manipulation within self-indexes, improving over previous methods.

Findings

Supports efficient concatenation of patterns in self-indexes

Compatible with many existing self-indexes

Offers space and time efficiency improvements

Abstract

Suppose we have just performed searches in a self-index for two patterns $A$ and $B$ and now we want to search for their concatenation \A B); how can we best make use of our previous computations? In this paper we consider this problem and, more generally, how we can store a dynamic library of patterns that we can easily manipulate in interesting ways. We give a space- and time-efficient data structure for this problem that is compatible with many of the best self-indexes.