Related papers: The Exact String Matching Problem: a Comprehensive…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
We consider the first problem that appears in any application of synchronizing automata, namely, the problem of deciding whether or not a given $n$-state $k$-letter automaton is synchronizing. First we generalize results from…
The aim of this note is to provide a reduction of the Exact Matching problem to the Top-$k$ Perfect Matching Problem. Together with earlier work by El Maalouly, this shows that the two problems are polynomial-time equivalent. The Exact…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
In recent years, significant advances have been made in the design and analysis of fully dynamic maximal matching algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
The classical pattern matching paradigm is that of seeking occurrences of one string - the pattern, in another - the text, where both strings are drawn from an alphabet set $\Sigma$. Assuming the text length is $n$ and the pattern length is…
Accelerating inexact string matching procedures is of utmost importance when dealing with practical applications where huge amount of data must be processed in real time, as usual in bioinformatics or cybersecurity. Inexact matching…