相关论文: Computing the BWT and LCP array of a Set of String…

We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…

Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…

Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Sorting extremely large datasets is a frequently occuring task in practice. These datasets are usually much larger than the computer's main memory; thus external memory sorting algorithms, first introduced by Aggarwal and Vitter (1988), are…

While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…

At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…

When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…

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 well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…

The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…

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…

A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…

Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…

The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…

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 recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…

Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external…

Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…

Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS)…