Related papers: Motif matching using gapped patterns
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Given a log and a specification, timed pattern matching aims at exhibiting for which start and end dates a specification holds on that log. For example, "a given action is always followed by another action before a given deadline". This…
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
We propose a new indexing structure for parameterized strings, called parameterized position heap. Parameterized position heap is applicable for parameterized pattern matching problem, where the pattern matches a substring of the text if…
A natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are $k$ background sequences, and each character in a background sequence is a random…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Term pattern matching is the problem of finding all pattern matches in a subject term, given a set of patterns. Finding efficient algorithms for this problem is an important direction for research [19]. We present a new set automaton…
Pattern matching is a powerful tool which is part of many functional programming languages as well as computer algebra systems such as Mathematica. Among the existing systems, Mathematica offers the most expressive pattern matching.…
Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…
Online string matching is a computational problem involving the search for patterns or substrings in a large text dataset, with the pattern and text being processed sequentially, without prior access to the entire text. Its relevance stems…