Related papers: Fast entropy-bounded string dictionary look-up wit…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
In this work, we present a literature review for full-text and keyword indexes as well as our contributions (which are mostly practice-oriented). The first contribution is the FM-bloated index, which is a modification of the well-known…
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…
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…
We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
Let us consider the Multiple String Matching Problem. In this problem, we consider a long string, denoted by $t$, of length $n$. This string is referred to as a text. We also consider a sequence of $m$ strings, denoted by $S$, which we…
The membership problem asks to maintain a set $S\subseteq[u]$, supporting insertions and membership queries, i.e., testing if a given element is in the set. A data structure that computes exact answers is called a dictionary. When a (small)…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
We study a document retrieval problem in the new framework where $D$ text documents are organized in a {\em category tree} with a pre-defined number $h$ of categories. This situation occurs e.g. with taxomonic trees in biology or subject…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
The $k$-mismatch problem consists in computing the Hamming distance between a pattern $P$ of length $m$ and every length-$m$ substring of a text $T$ of length $n$, if this distance is no more than $k$. In many real-world applications, any…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…