相关论文: Space-Efficient Computation of the LCP Array from …

The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

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…

In this paper we address the longest common extension (LCE) problem: to compute the length $\ell$ of the longest common prefix between any two suffixes of $T\in \Sigma^n$ with $ \Sigma = \{0, \ldots \sigma-1\} $. We present two fast and…

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…

Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…

Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…

In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…

In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…

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…

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ 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…

The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…

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…

The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…

The suffix array and the suffix tree are the two most fundamental data structures for string processing. For a length-$n$ text, however, they use $\Theta(n \log n)$ bits of space, which is often too costly. To address this, Grossi and…

In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…

We propose a B tree representation storing $n$ keys, each of $k$ bits, in either (a) $nk + O(nk / \lg n)$ bits or (b) $nk + O(nk \lg \lg n/ \lg n)$ bits of space supporting all B tree operations in either (a) $O(\lg n )$ time or (b) $O(\lg…

Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…

Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…