相关论文: Inducing the LCP-Array

Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…

Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. We consider two problems for a read-only string of length $N$ over an integer alphabet $[1, \dots, \sigma]$ for…

Pattern matching queries on strings can be solved in linear time by Knuth-Morris-Pratt (KMP) algorithm. In 1973, Weiner introduced the suffix tree of a string [FOCS 1973] and showed that the seemingly more difficult problem of computing…

The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…

In the past thirty years, numerous algorithms for building the suffix array of a string have been proposed. In 2021, the notion of suffix array was extended from strings to DFAs, and it was shown that the resulting data structure can be…

Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…

Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…

Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…

Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…

Given a text $T$ of length $n$, we propose a deterministic online algorithm computing the sparse suffix array and the sparse longest common prefix array of $T$ in $O(c \sqrt{\lg n} + m \lg m \lg n \lg^* n)$ time with $O(m)$ words of space…

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…

Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…

We first describe three algorithms for computing the Lyndon array that have been suggested in the literature, but for which no structured exposition has been given. Two of these algorithms execute in quadratic time in the worst case, the…

We present a new, simple, and efficient approach for computing the Lempel-Ziv (LZ77) factorization of a string in linear time, based on suffix arrays. Computational experiments on various data sets show that our approach constantly…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…

Given a string on an integer alphabet, we present an algorithm that computes the set of all distinct squares belonging to this string in time linear to the string length. As an application, we show how to compute the tree topology of the…

This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…

Suffix trees are key and efficient data structure for solving string problems. A suffix tree is a compressed trie containing all the suffixes of a given text of length $n$ with a linear construction cost. In this work, we introduce an…