About: An OpenMP-based tool for finding longest common subsequence in bioinformatics

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	An OpenMP-based tool for finding longest common subsequence in bioinformatics
Creator	Hu, Pingzhao Irani, Pourang Shikder, Rayhan Thulasiraman, Parimala
topic	covid:d33624f8b27d81d663f54d3e167aaf15968ff8a4#this
source	PMC
abstract	OBJECTIVE: Finding the longest common subsequence (LCS) among sequences is NP-hard. This is an important problem in bioinformatics for DNA sequence alignment and pattern discovery. In this research, we propose new CPU-based parallel implementations that can provide significant advantages in terms of execution times, monetary cost, and pervasiveness in finding LCS of DNA sequences in an environment where Graphics Processing Units are not available. For general purpose use, we also make the OpenMP-based tool publicly available to end users. RESULT: In this study, we develop three novel parallel versions of the LCS algorithm on: (i) distributed memory machine using message passing interface (MPI); (ii) shared memory machine using OpenMP, and (iii) hybrid platform that utilizes both distributed and shared memory using MPI-OpenMP. The experimental results with both simulated and real DNA sequence data show that the shared memory OpenMP implementation provides at least two-times absolute speedup than the best sequential version of the algorithm and a relative speedup of almost 7. We provide a detailed comparison of the execution times among the implementations on different platforms with different versions of the algorithm. We also show that removing branch conditions negatively affects the performance of the CPU-based parallel algorithm on OpenMP platform.
has issue date	2019-04-11(xsd:dateTime)
bibo:doi	10.1186/s13104-019-4256-6
bibo:pmid	30971295
has license	cc-by
sha1sum (hex)	d33624f8b27d81d663f54d3e167aaf15968ff8a4
schema:url	https://doi.org/10.1186/s13104-019-4256-6
resource representing a document's title	An OpenMP-based tool for finding longest common subsequence in bioinformatics
has PubMed Central identifier	PMC6458724
has PubMed identifier	30971295
schema:publication	BMC Res Notes
resource representing a document's body	covid:d33624f8b27d81d663f54d3e167aaf15968ff8a4#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/d33624f8b27d81d663f54d3e167aaf15968ff8a4
is schema:about of	named entity 'problem' named entity 'Graphics' named entity 'sequence alignment' named entity 'IMPORTANT PROBLEM' named entity 'USERS' named entity 'DNA SEQUENCES' named entity 'TOOL' named entity 'LONGEST' named entity 'NEW' named entity 'FINDING' named entity 'PURPOSE' named entity 'BASED' named entity 'DISCOVERY' named entity 'BIOINFORMATICS' named entity 'DNA SEQUENCE ALIGNMENT' named entity 'TERMS' named entity 'MAKE' named entity 'EXECUTION' named entity 'PATTERN' named entity 'OBJECTIVE' named entity 'LCS' named entity 'USE' named entity 'GRAPHICS' named entity 'TOOL' named entity 'COMMON' named entity 'FINDING' named entity 'COMMON' named entity 'PROVIDE' named entity 'WHERE' named entity 'ENVIRONMENT' named entity 'COST' named entity 'PROCESSING' named entity 'AVAILABLE' named entity 'LONGEST' named entity 'BIOINFORMATICS' named entity 'END' named entity 'GENERAL' named entity 'CPU' named entity 'RESEARCH' named entity 'UNITS' named entity 'SEQUENCES' named entity 'NOT AVAILABLE' named entity 'HARD' named entity 'TIMES' named entity 'PARALLEL' named entity 'BASED' named entity 'MONETARY' named entity 'SIGNIFICANT' covid:arg/d33624f8b27d81d663f54d3e167aaf15968ff8a4 named entity 'times' named entity 'advantages' named entity 'Objective' named entity 'parallel' named entity 'discovery' named entity 'longest common subsequence' named entity 'general purpose' named entity 'OpenMP' named entity 'MPI' named entity 'benchmarking' named entity 'DNA sequence alignment' named entity 'MPI' named entity 'Graphics Processing Unit' named entity 'algorithm' named entity 'NCBI' named entity 'base pairs' named entity 'antidiagonal' named entity 'algorithm' named entity 'DNA sequences' named entity 'parallelization' named entity 'base pairs' named entity 'DNA sequence data' named entity 'OpenMP' named entity 'CPUs' named entity 'OpenMP' named entity 'LCS' named entity 'sequence data'

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