Related papers: Constructing Suffixient Arrays Revisited
The LCP array is an important tool in stringology, allowing to speed up pattern matching algorithms and enabling compact representations of the suffix tree. Recently, Conte et al. [DCC 2023] and Cotumaccio et al. [SPIRE 2023] extended the…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…
The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a string $T$ of length $n$ has $O(n)$ nodes and edges, and the string label of each edge is encoded by a pair of positions in $T$.…
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…
A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…
We propose a new indexing structure for parameterized strings, called parameterized position heap. Parameterized position heap is applicable for parameterized pattern matching problem, where the pattern matches a substring of the text if…
Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string…