{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T12:12:25Z","timestamp":1771330345513,"version":"3.50.1"},"publisher-location":"Cham","reference-count":21,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783030445331","type":"print"},{"value":"9783030445348","type":"electronic"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-3-030-44534-8_23","type":"book-chapter","created":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T06:03:05Z","timestamp":1585116185000},"page":"298-313","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["A Block-Based Systolic Array on an HBM2 FPGA for DNA Sequence Alignment"],"prefix":"10.1007","author":[{"given":"Riadh","family":"Ben Abdelhamid","sequence":"first","affiliation":[]},{"given":"Yoshiki","family":"Yamaguchi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,3,25]]},"reference":[{"issue":"3","key":"23_CR1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403\u2013410 (1990)","journal-title":"J. Mol. Biol."},{"key":"23_CR2","doi-asserted-by":"crossref","unstructured":"Chen, P., Wang, C., Li, X., Zhou, X.: Hardware acceleration for the banded Smith-Waterman algorithm with the cycled systolic array, pp. 480\u2013481, December 2013","DOI":"10.1109\/FPT.2013.6718421"},{"key":"23_CR3","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s12859-016-0930-z","volume":"17","author":"J Daily","year":"2016","unstructured":"Daily, J.: Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinform. 17, 81 (2016). \nhttps:\/\/doi.org\/10.1186\/s12859-016-0930-z","journal-title":"BMC Bioinform."},{"key":"23_CR4","doi-asserted-by":"publisher","unstructured":"Di Tucci, L., O\u2019Brien, K., Blott, M., Santambrogio, M.: Architectural optimizations for high performance and energy efficient Smith-Waterman implementation on FPGAS using OpenCL, pp. 716\u2013721, March 2017. \nhttps:\/\/doi.org\/10.23919\/DATE.2017.7927082","DOI":"10.23919\/DATE.2017.7927082"},{"issue":"1","key":"23_CR5","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1007\/s12539-017-0225-8","volume":"10","author":"X Fei","year":"2017","unstructured":"Fei, X., Dan, Z., Lina, L., Xin, M., Chunlei, Z.: FPGASW: accelerating large-scale Smith\u2013Waterman sequence alignment application with backtracking on FPGA linear systolic array. Interdisc. Sci. Comput. Life Sci. 10(1), 176\u2013188 (2017). \nhttps:\/\/doi.org\/10.1007\/s12539-017-0225-8","journal-title":"Interdisc. Sci. Comput. Life Sci."},{"key":"23_CR6","unstructured":"Hasan, L., Khawaja, Y., Bais, A.: A systolic array architecture for the Smith-Waterman algorithm with high performance cell design, pp. 35\u201344, January 2008"},{"key":"23_CR7","doi-asserted-by":"crossref","unstructured":"Houtgast, E., Sima, V., Al-Ars, Z.: High performance streaming Smith-Waterman implementation with implicit synchronization on intel FPGA using OpenCL, December 2017","DOI":"10.1109\/BIBE.2017.000-6"},{"key":"23_CR8","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1109\/MC.1982.1653825","volume":"15","author":"H Kung","year":"1982","unstructured":"Kung, H.: Why systolic architectures? Computer 15, 37\u201346 (1982)","journal-title":"Computer"},{"key":"23_CR9","doi-asserted-by":"publisher","unstructured":"Liu, Y., et al.: Cudasw++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinform. 14 (2013). Article no. 117, \nhttps:\/\/doi.org\/10.1186\/1471-2105-14-117","DOI":"10.1186\/1471-2105-14-117"},{"issue":"3","key":"23_CR10","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443\u2013453 (1970)","journal-title":"J. Mol. Biol."},{"key":"23_CR11","unstructured":"Nurdin, D., et al.: High performance systolic array core architecture design for DNA sequencer. MATEC Web Conf. 150 (2018). Article no. 06009"},{"key":"23_CR12","doi-asserted-by":"publisher","unstructured":"Rognes, T.: Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinform. 12 (2011). \nhttps:\/\/doi.org\/10.1186\/1471-2105-12-221","DOI":"10.1186\/1471-2105-12-221"},{"key":"23_CR13","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/s12918-018-0614-6","volume":"12","author":"E Rucci","year":"2018","unstructured":"Rucci, E., et al.: SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences. BMC Syst. Biol. 12, 96 (2018). \nhttps:\/\/doi.org\/10.1186\/s12918-018-0614-6","journal-title":"BMC Syst. Biol."},{"key":"23_CR14","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1177\/1094342016654215","volume":"32","author":"E Rucci","year":"2016","unstructured":"Rucci, E., Garcia, C., Botella, G., De Giusti, A., Naiouf, M., Prieto Matias, M.: OSWALD: OpenCL Smith-Waterman on Altera\u2019s FPGA for large protein databases. Int. J. High Perform. Comput. Appl. 32, 337\u2013350 (2016). \nhttps:\/\/doi.org\/10.1177\/1094342016654215","journal-title":"Int. J. High Perform. Comput. Appl."},{"key":"23_CR15","unstructured":"Sandes, E., et al.: CUDAlign 3.0: parallel biological sequence comparison in large GPU clusters, pp. 160\u2013169, May 2014"},{"key":"23_CR16","doi-asserted-by":"publisher","first-page":"2838","DOI":"10.1109\/TPDS.2016.2515597","volume":"27","author":"E Sandes","year":"2016","unstructured":"Sandes, E., et al.: CUDAlign 4.0: incremental speculative traceback for exact chromosome-wide alignment in GPU clusters. IEEE Trans. Parallel Distrib. Syst. 27, 2838\u20132850 (2016)","journal-title":"IEEE Trans. Parallel Distrib. Syst."},{"key":"23_CR17","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"T Smith","year":"1981","unstructured":"Smith, T., Waterman, M.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195\u20137 (1981)","journal-title":"J. Mol. Biol."},{"key":"23_CR18","unstructured":"Xilinx: Alveo U280 Data Center Accelerator Card. \nhttps:\/\/www.xilinx.com\/products\/boards-and-kits\/alveo\/u280.html#specifications\n\n. Accessed 8 Dec 2019"},{"key":"23_CR19","unstructured":"Xilinx: Vivado HLS Optimization Methodology Guide. \nhttps:\/\/www.xilinx.com\/support\/documentation\/sw_manuals\/xilinx2018_1\/ug1270-vivado-hls-opt-methodology-guide.pdf\n\n. Accessed 8 Dec 2019"},{"key":"23_CR20","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1007\/978-3-642-19475-7_20","volume-title":"Reconfigurable Computing: Architectures, Tools and Applications","author":"Y Yamaguchi","year":"2011","unstructured":"Yamaguchi, Y., Tsoi, H.K., Luk, W.: FPGA-based Smith-Waterman algorithm: analysis and novel design. In: Koch, A., Krishnamurthy, R., McAllister, J., Woods, R., El-Ghazawi, T. (eds.) ARC 2011. LNCS, vol. 6578, pp. 181\u2013192. Springer, Heidelberg (2011). \nhttps:\/\/doi.org\/10.1007\/978-3-642-19475-7_20"},{"issue":"12","key":"23_CR21","doi-asserted-by":"publisher","first-page":"e82138","DOI":"10.1371\/journal.pone.0082138","volume":"8","author":"M Zhao","year":"2013","unstructured":"Zhao, M., et al.: SSW library: an SIMD Smith-Waterman C\/C++ library for use in genomic applications. PLoS ONE 8(12), e82138 (2013)","journal-title":"PLoS ONE"}],"container-title":["Lecture Notes in Computer Science","Applied Reconfigurable Computing. Architectures, Tools, and Applications"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-44534-8_23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,29]],"date-time":"2020-07-29T16:10:43Z","timestamp":1596039043000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-44534-8_23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9783030445331","9783030445348"],"references-count":21,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-44534-8_23","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"25 March 2020","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"ARC","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Symposium on Applied Reconfigurable Computing","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Toledo","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2020","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"1 April 2020","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"3 April 2020","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"16","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"arc2020","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/arcoresearch.com\/arc2020\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Double-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"40","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"18","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"45% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"4","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"11 poster presentations","order":10,"name":"additional_info_on_review_process","label":"Additional Info on Review Process","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}