A shared memory method for enhancing the HTNGH algorithm performance: Proposed method

Muhannad A. Abu-Hashem, Diaa M. Uliyan, Abdelrahman Abuarqoub

Allbwn ymchwil: Pennod mewn Llyfr/Adroddiad/Trafodion CynhadleddCyfraniad mewn cynhadleddadolygiad gan gymheiriaid

2 Dyfyniadau (Scopus)

Crynodeb

In bioinformatics, pair-wise alignment plays a significant role insequence comparison by rating the similarities and distances between protein, DeoxyriboNucleic Acid (DNA), and RiboNucleic Acid (RNA)sequences. Sequence comparison considered as a key stone in building distance matrices.Due to the rapid growth of molecular databases, the need for faster sequence comparison and alignment has become anecessity.High performance computing impacthas increased in the last decade through providing many high performance architectures and tools. In this paper we present a parallel shared memory design for a dynamic programming algorithm named Hash Table-N-Gram-Hirschberg (HT-NGH) an extension of Hashing-N-Gram-Hirschberg (HNGH) and N-Gram-Hirschberg (NGH) algorithm, to speed up the sequence alignment construction process.The focus of the proposed method ison the transformation phase of HT-NGH algorithm since it takes% of HT-NGH overall run time.The experimental evaluation of the proposed parallel designshows an enhancement in the execution time and speedup without sacrificing the accuracy. However,the decomposition method might slightly slowdown the proposed algorithm due to the differences in performance between the processing units.

Iaith wreiddiolSaesneg
TeitlProceedings of the International Conference on Future Networks and Distributed Systems, ICFNDS 2017
CyhoeddwrAssociation for Computing Machinery
ISBN (Electronig)9781450348447
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 19 Gorff 2017
Cyhoeddwyd yn allanolIe
Digwyddiad2017 International Conference on Future Networks and Distributed Systems, ICFNDS 2017 - Cambridge, Y Deyrnas Unedig
Hyd: 19 Gorff 201720 Gorff 2017

Cyfres gyhoeddiadau

EnwACM International Conference Proceeding Series
CyfrolPart F130522

Cynhadledd

Cynhadledd2017 International Conference on Future Networks and Distributed Systems, ICFNDS 2017
Gwlad/TiriogaethY Deyrnas Unedig
DinasCambridge
Cyfnod19/07/1720/07/17

Dyfynnu hyn