High performance systolic array core architecture design for DNA sequencer
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EDP Sciences
2020
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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 |
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Universiti Malaysia Perlis |
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| language |
English |
| topic |
Systolic array (SA) Deoxyribonucleic Acid (DNA) DNA sequencer |
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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 |
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1698698571925159936 |