Record link: 
http://hdl.handle.net/20.500.12708/192192
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Title: 
ISMatch: A real-time hardware accelerator for inexact string matching of DNA sequences on FPGA
en
Citation: 
Marchisio, A., Teodonio, F., Rizzi, A., & Shafique, M. (2023). ISMatch: A real-time hardware accelerator for inexact string matching of DNA sequences on FPGA. Microprocessors and Microsystems, 97, Article 104763. https://doi.org/10.1016/j.micpro.2023.104763
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Publisher DOI: 
10.1016/j.micpro.2023.104763
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Publication Type: 
Article - Original Research Article
en
Language: 
English
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Authors: 
Marchisio, Alberto 
Teodonio, Federico 
Rizzi, Antonello 
Shafique, Muhammad 
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Organisational Unit: 
E191-02 - Forschungsbereich Embedded Computing Systems 
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Journal: 
Microprocessors and Microsystems 
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ISSN: 
0141-9331
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Date (published): 
2023
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Number of Pages: 
10
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Publisher: 
ELSEVIER
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Peer reviewed: 
Yes
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Keywords: 
DNA sequence; Energy efficiency; FPGA; Hardware accelerator; Hardware design; High Level Synthesis; Inexact string matching; Levenshtein distance; Performance
en
Abstract: 
Since DNA strings suffer from variations like mutation, noisy sampling, and transmission, instead of searching for the exact match, the inexact string matching (ISM) of DNA sequences is preferred. Due to the large amount of data and massive data-dependency, the ISM algorithm is not suitable for being implemented into a general-purpose hardware. Towards this, we propose ISMatch, a novel specialized hardware architecture for computing the ISM in a fast and energy-efficient way. Our implementation on a Xilinx Ultrascale+ FPGA shows up to 70× and 2.2× clock cycles reduction compared to the ARM-based and the HLS implementations, respectively.
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Research Areas: 
Computer Engineering and Software-Intensive Systems: 100%
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Science Branch: 
1020 - Informatik: 100%
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