Related papers: Motif matching using gapped patterns
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method…
Motifs are the fundamental components of complex systems. The topological structure of networks representing complex systems and the frequency and distribution of motifs in these networks are intertwined. The complexities associated with…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
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…
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…
In the last fifteen years, data series motif and discord discovery have emerged as two useful and well-used primitives for data series mining, with applications to many domains, including robotics, entomology, seismology, medicine, and…
The primary objective of graph pattern matching is to find all appearances of an input graph pattern query in a large data graph. Such appearances are called matches. In this paper, we are interested in finding matches of interaction…
In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
In this thesis we develop tools for effective and flexible pattern matching. We introduce a new pattern matching system called amethyst. Amethyst is not only a generator of parsers of programming languages, but can also serve as an…
Interaction nets are a form of restricted graph rewrite system that can serve as a graphical or textual programming language. As such, benefits include one-step confluence, ease of parallelism and explicit garbage collection. However, some…
Motivation: Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in the field of comparative genomics and proteomics. However, current approaches lack a direct method for…
Matching pursuits are a class of greedy algorithms commonly used in signal processing, for solving the sparse approximation problem. They rely on an atom selection step that requires the calculation of numerous projections, which can be…
Cadences are structurally maximal arithmetic progressions of indices corresponding to equal characters in an underlying string. This paper provides a polynomial time detection algorithm for 3-cadences in grammar-compressed binary strings.…
In this paper, we study the problem of map matching with travel time constraints. Given a sequence of $k$ spatio-temporal measurements and an embedded path graph with travel time costs, the goal is to snap each measurement to a close-by…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…
Knowing who follows whom and what patterns they are following are crucial steps to understand collective behaviors (e.g. a group of human, a school of fish, or a stock market). Time series is one of resources that can be used to get insight…