Results 1 to 10 of about 735,070 (175)

Scalable Parallel Suffix Array Construction [PDF]

Parallel Computing, 2006
Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction.
Kulla, F., Sanders, P.
openaire   +4 more sources

Characterization of Graphs Without Even F $F$‐Orientations

Journal of Graph Theory, EarlyView.
ABSTRACT A graph G $G$ is 1‐extendable if every edge belongs to at least one 1‐factor of G $G$. Let G $G$ be a graph with a 1‐factor F $F$. Then an even (odd) F $F$ ‐orientation of G $G$ is an orientation in which each F $F$‐alternating cycle has exactly an even (odd) number of edges directed in the same fixed direction around the cycle.
Marién Abreu, Domenico Labbate, Federico Romaniello, John Sheehan   +3 more
wiley   +1 more source

Approximate String Matching with Compressed Indexes

Algorithms, 2009
A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T. It can also reproduce any substring of T, thus actually replacing T. Despite the recent explosion of interest on compressed
Pedro Morales, Arlindo L. Oliveira, Luís M. S. Russo, Gonzalo Navarro   +3 more
doaj   +1 more source

Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments. [PDF]

PLoS ONE, 2012
PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large ...
David A Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A Celena Carrillo, Peter L Williams, Shea N Gardner   +5 more
doaj   +1 more source

Strain Rate Angle Distribution as an Indicator of Post‐Infarct Myocardial Remodeling: Proof‐of‐Concept of a Novel Application of the MRI Derived Strain Rate Tensor Field

Magnetic Resonance in Medicine, EarlyView.
ABSTRACT Purpose Left ventricular (LV) strain is an early indicator of myocardial dysfunction. However, conventional strain metrics do not fully account for the multidirectional nature of myocardial deformation. The strain rate tensor, derived from velocity‐encoded MRI, represents the time‐resolved magnitude and direction of strain rate without the ...
Lasse Totland, Bård A. Bendiksen, Einar S. Nordén, Ida Marie Hauge‐Iversen, Kaja Knudsen Bergo, Lili Zhang, Ivar Sjaastad, Emil K. S. Espe   +7 more
wiley   +1 more source

The new approach of multiple genome sequence matching based on GPU

四川大学学报. 自然科学版, 2017
Suffix trees and suffix arrays have been used widely in bioinformatics applications, especially for DNA sequence alignments in the initial exact match phase of heuristic algorithms.
DING Sha, ZHAO Shi-Yuan, LIN Tao
doaj  

Direct construction of sparse suffix arrays with Libsais

BMC Bioinformatics
Background Pattern matching is a fundamental challenge in bioinformatics, especially in the fields of genomics, transcriptomics and proteomics. Efficient indexing structures, such as suffix arrays, are critical for searching large datasets.
Simon Van de Vyver, Tibo Vande Moortele, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt   +4 more
doaj   +1 more source

A Fast Algorithm for the Largest Area First Parsing of Real Strings

IEEE Access, 2020
The largest area first parsing of a string often leads to the best results in grammar compression for a variety of input data. However, the fastest existing algorithm has Θ(N2 log N) time complexity, which makes it impractical for real-life ...
Ivan Katanic, Strahil Ristov, Martin Rosenzweig   +2 more
doaj   +1 more source

Smaller Compressed Suffix Arrays†

The Computer Journal, 2020
AbstractAn alternative to compressed suffix arrays is introduced, based on representing a sequence of integers using Fibonacci encodings, thereby reducing the space requirements of state-of-the-art implementations of the suffix array, while retaining the searching functionalities.
Ekaterina Benza, Shmuel T. Klein, Dana Shapira   +2 more
openaire   +2 more sources

Online Rebate Strategy for a Dual‐Channel Supply Chain

Naval Research Logistics (NRL), EarlyView.
ABSTRACT As online shopping channels become ubiquitous, consumers are faced with a vast number of digital purchasing options. To attract more consumers, many e‐shops utilize cashback websites (CWs) to provide online rebates. This study examines a dual‐channel supply chain, in which the manufacturer sells products through both its own online store and a
Peng Xu, Xuan Zhao, Tiaojun Xiao
wiley   +1 more source