Related papers: In-Place Sparse Suffix Sorting
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
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 consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…
The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…
We present several modifications to the previously proposed MSPP algorithm that can speed-up its execution considerably. The MSPP algorithm leverages a multiscale representation of the environment in $n$ dimensions. The information of the…
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…
The suffix array is the key to efficient solutions for myriads of string processing problems in different applications domains, like data compression, data mining, or Bioinformatics. With the rapid growth of available data, suffix array…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
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…
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…
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…
Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…
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…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…
We present an extension of the in-place BWT algorithm of Crochemore et al. [8] that enables the construction of the Lyndon array using O(1) extra space. Our approach incrementally maintains the lexicographic ranks of the suffixes during the…
We propose a simple linear-time on-line algorithm for constructing a position heap for a string [Ehrenfeucht et al, 2011]. Our definition of position heap differs slightly from the one proposed in [Ehrenfeucht et al, 2011] in that it…
Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…