Related papers: Motif matching using gapped patterns
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently,…
With the widespread application of efficient pattern mining algorithms, sequential patterns that allow gap constraints have become a valuable tool to discover knowledge from biological data such as DNA and protein sequences. Among all kinds…
The timed pattern matching problem is formulated by Ulus et al. and has been actively studied since, with its evident application in monitoring real-time systems. The problem takes as input a timed word/signal and a timed pattern (specified…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif,…
We study the "set parameterized matching" problem, a generalization of the classical parameterized matching problem introduced by Baker. In set parameterized matching, both the pattern and text are sequences where each position contains a…
Non-free data types are data types whose data have no canonical forms. For example, multisets are non-free data types because the multiset $\{a,b,b\}$ has two other equivalent but literally different forms $\{b,a,b\}$ and $\{b,b,a\}$.…
We consider algorithms for finding and counting small, fixed graphs in sparse host graphs. In the non-sparse setting, the parameters treedepth and treewidth play a crucial role in fast, constant-space and polynomial-space algorithms…
The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment…
Many tasks in data mining and related fields can be formalized as matching between objects in two heterogeneous domains, including collaborative filtering, link prediction, image tagging, and web search. Machine learning techniques,…
Haskell is a popular choice for hosting deeply embedded languages. A recurring challenge for these embeddings is how to seamlessly integrate user defined algebraic data types. In particular, one important, convenient, and expressive feature…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
Pattern counting in graphs is fundamental to network science tasks, and there are many scalable methods for approximating counts of small patterns, often called motifs, in large graphs. However, modern graph datasets now contain richer…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
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 pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
Graph pattern matching algorithms to handle million-scale dynamic graphs are widely used in many applications such as social network analytics and suspicious transaction detections from financial networks. On the other hand, the computation…
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…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…