Finding All-Pairs Suffix-Prefix Matching Using Suffix Array

Algorithm Engineering for All-Pairs Suffix-Prefix Matching

All-pairs suffix-prefix matching is an important part of DNA sequence assembly where it is the most time-consuming part of the whole assembly. Although there are algorithms for all-pairs suffix-prefix matching which are optimal in the asymptotic time complexity, they are slower than SOF and Readjoiner which are state-of-the-art algorithms used in practice. In this paper we present an algorithm ...

Approximate All-Pairs Suffix/Prefix Overlaps

Finding approximate overlaps is the first phase of many sequence assembly methods. Given a set of r strings of total length n and an error-rate , the goal is to find, for all-pairs of strings, their suffix/prefix matches (overlaps) that are within edit distance k = d `e, where ` is the length of the overlap. We propose new solutions for this problem based on backward backtracking (Lam et al. 20...

Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem

The all-pairs suffix-prefix matching problem is a basic problem in string processing. It has an application in the de novo genome assembly task, which is one of the major bioinformatics problems. Due to the large size of the input data, it is crucial to use fast and space efficient solutions. In this paper, we present a space-economical solution to this problem using the generalized Sadakane co...

Bounded Prefix-Suffix Duplication

Abs t r ac t . We consider a restricted variant of the prefix-sufñx duplication operation, called bounded prefix-sufñx duplication. It consists in the iterative duplication of a prefix or suffix, whose length is bounded by a constant, of a given word. We give a sufncient condition for the closure under bounded prefix-sufñx duplication of a class of languages. Consequently, the class of regular ...

Prefix-suffix duplication