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High performance systolic array core architecture design for DNA sequencer

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Main Authors: Dayana, Saiful Nurdin, Mohd. Nazrin, Md. Isa, Rizalafande, Che Ismail, Muhammad Imran, Ahmad
Other Authors: nazrin@unimap.edu.my
Format: Article
Language:English
Published: EDP Sciences 2020
Subjects:
Systolic array (SA)
Deoxyribonucleic Acid (DNA)
DNA sequencer
Online Access:http://dspace.unimap.edu.my:80/xmlui/handle/123456789/69198
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spelling my.unimap-691982020-12-31T01:24:35Z High performance systolic array core architecture design for DNA sequencer Dayana, Saiful Nurdin Mohd. Nazrin, Md. Isa Rizalafande, Che Ismail Muhammad Imran, Ahmad nazrin@unimap.edu.my Systolic array (SA) Deoxyribonucleic Acid (DNA) DNA sequencer Link to publisher's homepage at https://www.matec-conferences.org/ This paper presents a high performance systolic array (SA) core architecture design for Deoxyribonucleic Acid (DNA) sequencer. The core implements the affine gap penalty score Smith-Waterman (SW) algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL) and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA) and improved in the core area by 90% reduction. 2020-12-31T01:24:35Z 2020-12-31T01:24:35Z 2018 Article MATEC Web of Conferences, vol.150, 2018, 6 pages 2261-236X (online) http://dspace.unimap.edu.my:80/xmlui/handle/123456789/69198 https://doi.org/10.1051/matecconf/201815006009 en Malaysia Technical Universities Conference on Engineering and Technology (MUCET 2017); EDP Sciences
institution Universiti Malaysia Perlis
building UniMAP Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Perlis
content_source UniMAP Library Digital Repository
url_provider http://dspace.unimap.edu.my/
language English
topic Systolic array (SA)
Deoxyribonucleic Acid (DNA)
DNA sequencer
spellingShingle Systolic array (SA)
Deoxyribonucleic Acid (DNA)
DNA sequencer
Dayana, Saiful Nurdin
Mohd. Nazrin, Md. Isa
Rizalafande, Che Ismail
Muhammad Imran, Ahmad
High performance systolic array core architecture design for DNA sequencer
description Link to publisher's homepage at https://www.matec-conferences.org/
author2 nazrin@unimap.edu.my
author_facet nazrin@unimap.edu.my
Dayana, Saiful Nurdin
Mohd. Nazrin, Md. Isa
Rizalafande, Che Ismail
Muhammad Imran, Ahmad
format Article
author Dayana, Saiful Nurdin
Mohd. Nazrin, Md. Isa
Rizalafande, Che Ismail
Muhammad Imran, Ahmad
author_sort Dayana, Saiful Nurdin
title High performance systolic array core architecture design for DNA sequencer
title_short High performance systolic array core architecture design for DNA sequencer
title_full High performance systolic array core architecture design for DNA sequencer
title_fullStr High performance systolic array core architecture design for DNA sequencer
title_full_unstemmed High performance systolic array core architecture design for DNA sequencer
title_sort high performance systolic array core architecture design for dna sequencer
publisher EDP Sciences
publishDate 2020
url http://dspace.unimap.edu.my:80/xmlui/handle/123456789/69198
_version_ 1698698571925159936
score 13.222552

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