Towards real-time DNA biometrics using GPU-accelerated processing

2020 ◽  
Author(s):  
Mario Reja ◽  
Ciprian Pungila ◽  
Viorel Negru
Keyword(s):  
Dna Sequences ◽  
Search Space ◽  
Careful Consideration ◽  
Computing Power ◽  
The Past ◽  
Graphical Processing Units ◽  
Massively Parallel Computing ◽  
Computationally Intensive ◽  
Graphical Processing ◽  
Specialized Hardware

Abstract Decoding the human genome in the past decades has brought into focus a computationally intensive operation through DNA profiling. The typical search space for these kinds of problems is extremely large and requires specialized hardware and algorithms to perform the necessary sequence analysis. In this paper, we propose an innovative and scalable approach to exact multi-pattern matching of nucleotide sequences by harnessing the massively parallel computing power found in commodity graphical processing units. Our approach places careful consideration on preprocessing of DNA datasets and runtime performance, while exploiting the full capabilities of the heterogeneous platform it runs on. Finally, we evaluate our models against real-world DNA sequences.

Using GPUs to compute fast Fourier transforms for crystal structure solution and refinement

2013 ◽  
Vol 46 (3) ◽  
pp. 594-600 ◽  
Author(s):  
ElSayed Mohamed Shalaby ◽  
Miguel Afonso Oliveira
Keyword(s):  
Crystal Structure ◽  
Fourier Transformation ◽  
Fourier Transforms ◽  
Fast Fourier Transformation ◽  
Parallel Calculations ◽  
The Past ◽  
Graphical Processing Units ◽  
Software Algorithms ◽  
Structure Solution ◽  
Graphical Processing

In the past few years, new hardware tools have become available for computing using the graphical processing units (GPUs) present in modern graphics cards. These GPUs allow efficient parallel calculations with a much higher throughput than microprocessors. In this work, fast Fourier transformation calculations used inSIR2011software algorithms have been carried out using the power of the GPU, and the speed of the calculations has been compared with that achieved using normal CPUs.

scholarly journals GPU Usage in ATLAS Reconstruction and Analysis

2020 ◽  
Vol 245 ◽  
pp. 05006
Author(s):  
Attila Krasznahorkay ◽  
Charles Leggett ◽  
Alaettin Serhan Mete ◽  
Scott Snyder ◽  
Vakho Tsulaia
Keyword(s):  
Data Model ◽  
Memory Management ◽  
High Performance ◽  
Event Data ◽  
Software Environment ◽  
The Past ◽  
Graphical Processing Units ◽  
Different Types ◽  
Graphical Processing ◽  
Performance Computing

With Graphical Processing Units (GPUs) and other kinds of accelerators becoming ever more accessible, High Performance Computing Centres all around the world using them ever more, ATLAS has to find the best way of making use of such accelerators in much of its computing. Tests with GPUs – mainly with CUDA – have been performed in the past in the experiment. At that time the conclusion was that it was not advantageous for the ATLAS offline and trigger software to invest time and money into GPUs. However as the usage of accelerators has become cheaper and simpler in recent years, their re-evaluation in ATLAS’s offline software is warranted. We show new results of using GPU accelerated calculations in ATLAS’s offline software environment using the ATLAS offline/analysis (xAOD) Event Data Model. We compare the performance and flexibility of a couple of the available GPU programming methods, and show how different memory management setups affect our ability to offload different types of calculations to a GPU efficiently.

A practical implementation of acoustic full waveform inversion on graphical processing units

2015 ◽  
Vol 6 (2) ◽  
pp. 5-16 ◽  
Author(s):  
Sergio Alberto Abreo Carrillo ◽  
Ana B. Ramirez ◽  
Oscar Reyes ◽  
David Leonardo Abreo-Carrillo ◽  
Herling González Alvarez
Keyword(s):  
Waveform Inversion ◽  
Practical Implementation ◽  
Full Waveform Inversion ◽  
Full Waveform ◽  
Graphical Processing Units ◽  
Graphical Processing

Detection of Flaviviral-Like DNA Sequences in Aedes aegypti (Diptera: Culicidae) Collected From Argentina

2021 ◽  
Author(s):  
Melisa B Bonica ◽  
Dario E Balcazar ◽  
Ailen Chuchuy ◽  
Jorge A Barneche ◽  
Carolina Torres ◽  
...  
Keyword(s):  
Public Health ◽  
Aedes Aegypti ◽  
Dna Sequences ◽  
Immature Stages ◽  
Public Health Burden ◽  
The Past ◽  
Health Burden ◽  
The World ◽  
Aegypti Genome ◽  
Dengue Epidemics

Abstract Diseases caused by flaviviruses are a major public health burden across the world. In the past decades, South America has suffered dengue epidemics, the re-emergence of yellow fever and St. Louis encephalitis viruses, and the introduction of West Nile and Zika viruses. Many insect-specific flaviviruses (ISFs) that cannot replicate in vertebrate cells have recently been described. In this study, we analyzed field-collected mosquito samples from six different ecoregions of Argentina to detect flaviviruses. We did not find any RNA belonging to pathogenic flaviviruses or ISFs in adults or immature stages. However, flaviviral-like DNA similar to flavivirus NS5 region was detected in 83–100% of Aedes aegypti (L.). Despite being previously described as an ancient element in the Ae. aegypti genome, the flaviviral-like DNA sequence was not detected in all Ae. aegypti samples and sequences obtained did not form a monophyletic group, possibly reflecting the genetic diversity of mosquito populations in Argentina.

scholarly journals Data Structures to Represent a Set of k -long DNA Sequences

2021 ◽  
Vol 54 (1) ◽  
pp. 1-22
Author(s):  
Rayan Chikhi ◽  
Jan Holub ◽  
Paul Medvedev
Keyword(s):  
Data Structures ◽  
Dna Sequences ◽  
Sequencing Data ◽  
String Algorithms ◽  
Fixed Length ◽  
The Past

The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k -mers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying a k -mer set has emerged as a shared underlying component. A set of k -mers has unique features and applications that, over the past 10 years, have resulted in many specialized approaches for its representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query a k -mer set. We hope this survey will serve as a resource for researchers in the field as well as make the area more accessible to researchers outside the field.

scholarly journals An advanced frequent closed sequences using BIDE

2018 ◽  
Vol 7 (2.20) ◽  
pp. 101
Author(s):  
K Vineela ◽  
M V.B.T. Santhi ◽  
N V.V. Gowtham Srujan ◽  
V Ashok
Keyword(s):  
Experimental Study ◽  
Search Engines ◽  
Historical Data ◽  
Search Space ◽  
Effective Algorithm ◽  
Direct Test ◽  
Test Strategy ◽  
The Past ◽  
Mining Algorithm ◽  
Parent Child Relationships

According to the past reasearches which produced few argumented stating that the frequent mining algorithm should only be closed but not frequent, as it not only results in compact but also complete results, and also in greater effectiveness. Most of the previous algorithms have mainly provided a direct test strategy to detect. In this article, we provide an Advanced BIDE, which is an effective algorithm used for processing query methods frequently closed. BI-Directional extension algorithm is better in pruning or filtering the search space when compared to any other algorithm. It is related to the calculation of frequent samples of search engines by parent-child relationships. An experimental study based on a variety of real historical data demonstrates the effectiveness and measurability of A-BIDE on the known alternatives of the past. It can also be scaled in terms of size of a query. 

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