HBLast: An open-source FPGA Library for DNA sequencing acceleration

Marzhan Bekbolat; Sabina Kairatova; Ayan Shymyrbay; Kizheppatt Vipin

doi:10.1109/IPDPSW.2019.00022

HBLast: An open-source FPGA Library for DNA sequencing acceleration

Marzhan Bekbolat, Sabina Kairatova, Ayan Shymyrbay, Kizheppatt Vipin

Electrical and Computer Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Scopus citations

Abstract

Biological sequence alignment algorithms work by identifying the degree of similarity between a newly discovered biological sequence with already known sequences. Exponential growth in the database and query sizes make pure softwarebased solutions inefficient in finding a solution within the time constraints. This calls for hardware acceleration-based solutions such as those based on field programmable gate arrays (FPGAs). In this work we present the design and implementation of the popular BLAST algorithm for nucleotide sequence alignment, called HBLast, targeting FPGA-based reconfigurable platforms.

Original language	English (US)
Title of host publication	Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	79-82
Number of pages	4
ISBN (Electronic)	9781728135106
DOIs	https://doi.org/10.1109/IPDPSW.2019.00022
State	Published - May 2019
Event	33rd IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019 - Rio de Janeiro, Brazil Duration: May 20 2019 → May 24 2019

Publication series

Name	Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019

Conference

Conference	33rd IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019
Country/Territory	Brazil
City	Rio de Janeiro
Period	05/20/19 → 05/24/19

Bibliographical note

Publisher Copyright:
© 2019 IEEE.

Keywords

BLAST algorithm
FPGA
Parallel architecture
Sequence alignment

ASJC Scopus subject areas

Information Systems and Management
Artificial Intelligence
Computer Networks and Communications
Hardware and Architecture
Control and Optimization

Access to Document

10.1109/IPDPSW.2019.00022

Cite this

Bekbolat, M., Kairatova, S., Shymyrbay, A., & Vipin, K. (2019). HBLast: An open-source FPGA Library for DNA sequencing acceleration. In Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019 (pp. 79-82). Article 8778371 (Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IPDPSW.2019.00022

Bekbolat, Marzhan ; Kairatova, Sabina ; Shymyrbay, Ayan et al. / HBLast : An open-source FPGA Library for DNA sequencing acceleration. Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 79-82 (Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019).

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abstract = "Biological sequence alignment algorithms work by identifying the degree of similarity between a newly discovered biological sequence with already known sequences. Exponential growth in the database and query sizes make pure softwarebased solutions inefficient in finding a solution within the time constraints. This calls for hardware acceleration-based solutions such as those based on field programmable gate arrays (FPGAs). In this work we present the design and implementation of the popular BLAST algorithm for nucleotide sequence alignment, called HBLast, targeting FPGA-based reconfigurable platforms.",

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year = "2019",

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Bekbolat, M, Kairatova, S, Shymyrbay, A & Vipin, K 2019, HBLast: An open-source FPGA Library for DNA sequencing acceleration. in Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019., 8778371, Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019, Institute of Electrical and Electronics Engineers Inc., pp. 79-82, 33rd IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019, Rio de Janeiro, Brazil, 05/20/19. https://doi.org/10.1109/IPDPSW.2019.00022

HBLast: An open-source FPGA Library for DNA sequencing acceleration. / Bekbolat, Marzhan; Kairatova, Sabina; Shymyrbay, Ayan et al.
Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019. Institute of Electrical and Electronics Engineers Inc., 2019. p. 79-82 8778371 (Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - Biological sequence alignment algorithms work by identifying the degree of similarity between a newly discovered biological sequence with already known sequences. Exponential growth in the database and query sizes make pure softwarebased solutions inefficient in finding a solution within the time constraints. This calls for hardware acceleration-based solutions such as those based on field programmable gate arrays (FPGAs). In this work we present the design and implementation of the popular BLAST algorithm for nucleotide sequence alignment, called HBLast, targeting FPGA-based reconfigurable platforms.

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Bekbolat M, Kairatova S, Shymyrbay A, Vipin K. HBLast: An open-source FPGA Library for DNA sequencing acceleration. In Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019. Institute of Electrical and Electronics Engineers Inc. 2019. p. 79-82. 8778371. (Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019). doi: 10.1109/IPDPSW.2019.00022

HBLast: An open-source FPGA Library for DNA sequencing acceleration

Abstract

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Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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