HBLast

An open-source FPGA Library for DNA sequencing acceleration

Marzhan Bekbolat, Sabina Kairatova, Ayan Shymyrbay, Kizheppatt Vipin

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 languageEnglish
Title of host publicationProceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages79-82
Number of pages4
ISBN (Electronic)9781728135106
DOIs
Publication statusPublished - May 1 2019
Event33rd IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019 - Rio de Janeiro, Brazil
Duration: May 20 2019May 24 2019

Publication series

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

Conference

Conference33rd IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019
CountryBrazil
CityRio de Janeiro
Period5/20/195/24/19

Fingerprint

DNA Sequencing
Sequence Alignment
Open Source
Field Programmable Gate Array
Field programmable gate arrays (FPGA)
DNA
Hardware Acceleration
Exponential Growth
Query
Nucleotides
Hardware
Libraries
Sequencing
Open source
Alignment
Design
Similarity

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

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). [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

HBLast : An open-source FPGA Library for DNA sequencing acceleration. / Bekbolat, Marzhan; Kairatova, Sabina; Shymyrbay, Ayan; Vipin, Kizheppatt.

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 proceedingConference contribution

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, 5/20/19. https://doi.org/10.1109/IPDPSW.2019.00022
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). https://doi.org/10.1109/IPDPSW.2019.00022
Bekbolat, Marzhan ; Kairatova, Sabina ; Shymyrbay, Ayan ; Vipin, Kizheppatt. / 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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