Related papers: Morphisms and BWT-run Sensitivity
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…
We study the problem of indexing and compressing tries using a BWT-based approach. Specifically, we consider a succinct and compressed representation of the XBWT of Ferragina et al.\ [FOCS '05, JACM '09] corresponding to the analogous of…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
We study how much injective morphisms can increase the repetitiveness of a given word. This question has a few possible variations depending on the meaning of ``repetitiveness''. We concentrate on fractional exponents of finite words and…
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…
The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…
In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…
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…
Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…
The notion of Wheeler languages is rooted in the Burrows-Wheeler transform (BWT), one of the most central concepts in data compression and indexing. The BWT has been generalized to finite automata, the so-called Wheeler automata, by Gagie…
In the era of deep learning, word embeddings are essential when dealing with text tasks. However, storing and accessing these embeddings requires a large amount of space. This is not conducive to the deployment of these models on…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
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…
We characterize those strings whose suffix arrays are based on arithmetic progressions, in particular, arithmetically progressed permutations where all pairs of successive entries of the permutation have the same difference modulo the…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…