Related papers: On building minimal automaton for subset matching …
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
In recent years, aligning a sequence to a pangenome has become a central problem in genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits…
We consider constrained minimization problems and propose to replace the projection onto the entire feasible region, required in the Projected Subgradient Method (PSM), by projections onto the individual sets whose intersection forms the…
In the range $\alpha$-majority query problem, we are given a sequence $S[1..n]$ and a fixed threshold $\alpha \in (0, 1)$, and are asked to preprocess $S$ such that, given a query range $[i..j]$, we can efficiently report the symbols that…
The dictionary matching is a task to find all occurrences of patterns in a set $D$ (called a dictionary) on a text $T$. The Aho-Corasick-automaton (AC-automaton) is a data structure which enables us to solve the dictionary matching problem…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
The Block Tree is a recently proposed data structure that reaches compression close to Lempel-Ziv while supporting efficient direct access to text substrings. In this paper we show how a self-index can be built on top of a Block Tree so…
Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of…
In this paper we study the adaptive prefix coding problem in cases where the size of the input alphabet is large. We present an online prefix coding algorithm that uses $O(\sigma^{1 / \lambda + \epsilon}) $ bits of space for any constants…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
Given $d$ strings over the alphabet $\{0,1,\ldots,\sigma{-}1\}$, the classical Aho--Corasick data structure allows us to find all $occ$ occurrences of the strings in any text $T$ in $O(|T| + occ)$ time using $O(m\log m)$ bits of space,…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…