Related papers: Practical combinations of repetition-aware data st…
We investigate properties of the bijective Burrows-Wheeler transform (BBWT). We show that for any string $w$, a bidirectional macro scheme of size $O(r_B)$ can be induced from the BBWT of $w$, where $r_B$ is the number of maximal character…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…
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…
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…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
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 Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
Converting a compressed format of a string into another compressed format without an explicit decompression is one of the central research topics in string processing. We discuss the problem of converting the run-length Burrows-Wheeler…
The Burrows-Wheeler Transform (BWT) is a fundamental component in many data structures for text indexing and compression, widely used in areas such as bioinformatics and information retrieval. The extended BWT (eBWT) generalizes the…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…