Related papers: A Comparative Study on String Matching Algorithm o…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…
This paper describes the software implementation of genetic algorithm for identifying and selecting most relevant results received during sequentially executed subject search operations. Simulated evolutionary process generates sustainable…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
String diagrams are an increasingly popular algebraic language for the analysis of graphical models of computations across different research fields. Whereas string diagrams have been thoroughly studied as semantic structures, much less…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Citation matching is a challenging task due to different problems such as the variety of citation styles, mistakes in reference strings and the quality of identified reference segments. The classic citation matching configuration used in…
Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
We study possible applications of artificial neural networks to examine the string landscape. Since the field of application is rather versatile, we propose to dynamically evolve these networks via genetic algorithms. This means that we…
We describe a seriation algorithm for ranking a set of items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Tasks that model the relation between pairs of tokens in a string are a vital part of understanding natural language. Such tasks, in general, require exhaustive pair-wise comparisons of tokens, thus having a quadratic runtime complexity in…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
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…