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The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known non-recursive ...

Reconstructing input from a data structure entails determining whether an instance of the data structure is in fact valid or not, and if valid, discovering the underlying data that it represents. In this paper we consider the parameterized suffix ...

The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the longest common prefixes for lexicographically ...

The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known non-...

Reconstructing input from a data structure entails determining whether an instance of the data structure is in fact valid or not, and if valid, discovering the underlying data that it represents. In this paper we consider the parameterized suffix ...${}^{\mathrm{}}$

Let two static sequences of strings P and S, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string T given in an online manner, ...${}_{}$$\mathrm{}$${}_{}$${}_{}$${}_{\mathrm{}}{}_{\mathrm{}}$$$$$${}_{}$${}_{}$$$${}_{}$$$${}_{}$${}_{}{}_{}$$$$$

Materialized views (MVs) are an elegant redundant optimization technique for analytical workloads. Numerous frameworks and algorithms for selecting MVs have been propounded, and some are deployed in commercial DBMSs. The central role of MVs in ...

The suffix array SA[1..n] of a text T of length n is a permutation of {1, …, n} describing the lexicographical ordering of suffixes of T and is considered to be one of the most important data structures for string processing, with dozens of applications ...

In structural pattern matching, two n-length strings X and Y over $\Sigma$ are said to match, if there exists a one-to-one function $f:\Sigma \to \Sigma$ such that (i) for $0\le i<n$, $f(X[i])=Y[i]$ and (ii) for any $x,y\in \Sigma$ whose complements are $x^{\prime }$ and $y^{\prime }$, respectively, if $f(x)=\mathrm{...}$${}^{}{}^{}$$\mathrm{}\mathrm{}$$$

The suffix array is a fundamental data structure for many applications that involve string searching and data compression. We obtain the first in-place suffix array construction algorithms that are optimal both in time and space for (...

This article proposes a succinct parallel algorithm, called pLZone, to compute the Lempel–Ziv (LZ77) factorization of a size-n input string over a constant alphabet in $\mathcal{O}(n)$ time using approximately a small n-word workspace, where each word ...$\mathrm{}$

While a suffix index built on a suffix array is capable of supporting full-text searches over any data, its search speed can be accelerated using a keyword index for the set of keywords extracted from data. We attempt to design a method for ...${}_{\mathrm{}}$

Given a text T and a set of r patterns P 1 , P 2 , … , P r, the exact multiple pattern matching problem reports the ending positions of all occurrences of P i in T for 1 ≤ i ≤ r. By transforming all substrings with a fixed length of T ...

We present a practical comparison of suffix array construction algorithms on modern hardware. The benchmark is conducted using our new benchmark framework SACABench, which allows for an easy deployment of publicly available implementations, simple ...

In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in O(n) time using words of working space, where n is the length of the ...

DNA sequencing technologies have tremendously increased their throughput, and hence complicated DNA assembly. Numerous assembly programs use de Bruijn graphs (dBG) built from short reads to merge these into contigs, which represent ...

The FM index (Ferragina and Manzini in J ACM 52(4):552---581, 2005) is a widely-used compressed data structure that stores a string T in a compressed form and also supports fast pattern matching queries. In this paper, we describe new FM-index variants ...

Sorting the suffixes of an input string is a fundamental task in many applications such as data compression, genome alignment, and full-text search. The induced sorting (IS) method has been successfully applied to design a number of state-of-the-art ...

We show how the longest common prefix (LCP) array can be generated as a by-product of the suffix array construction algorithm SACA-K (Nong, 2013). Our algorithm builds on Fischer's proposal (Fischer, WADS'11), and also runs in linear time, but uses only ...

Novel twin binary Burrows-Wheeler type transforms are introduced.The transforms are defined for Lyndon-like B-words which apply binary block order.We call this approach the B-BWT Rouen Transform.These bijective Rouen Transforms and inverses are computed ...