Related papers: Practical combinations of repetition-aware data st…
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit…
Regular expression matching is of practical importance due to its widespread use in real-world applications. In practical use, regular expressions are often used with real-world extensions. Accordingly, the matching problem of regular…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
Relative Lempel-Ziv (RLZ) parsing is a dictionary compression method in which a string $S$ is compressed relative to a second string $R$ (called the reference) by parsing $S$ into a sequence of substrings that occur in $R$. RLZ is…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
The Burrows-Wheeler-Transform (BWT) is an invertible permutation of a text known to be highly compressible but also useful for sequence analysis, what makes the BWT highly attractive for lossless data compression. In this paper, we present…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
Compression is beneficial because it helps detract resource usage. It reduces data storage space as well as transmission traffic and improves web pages loading. Run-length coding (RLC) is a lossless data compression algorithm. Data are…
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
This paper provides an upper bound for several subsets of maximal repeats and maximal pairs in compressed strings and also presents a formerly unknown relationship between maximal pairs and the run-length Burrows-Wheeler transform. This…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…
Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that…
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…