{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T15:34:00Z","timestamp":1772724840306,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":59,"publisher":"ACM","license":[{"start":{"date-parts":[[2020,5,30]],"date-time":"2020-05-30T00:00:00Z","timestamp":1590796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2020,5,30]]},"DOI":"10.1145\/3383669.3398279","type":"proceedings-article","created":{"date-parts":[[2020,5,30]],"date-time":"2020-05-30T12:25:03Z","timestamp":1590841503000},"page":"36-48","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":41,"title":["BioSEAL"],"prefix":"10.1145","author":[{"given":"Roman","family":"Kaplan","sequence":"first","affiliation":[{"name":"Technion, Israel"}]},{"given":"Leonid","family":"Yavits","sequence":"additional","affiliation":[{"name":"Technion, Israel"}]},{"given":"Ran","family":"Ginosasr","sequence":"additional","affiliation":[{"name":"Technion, Israel"}]}],"member":"320","published-online":{"date-parts":[[2020,5,30]]},"reference":[{"key":"e_1_3_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1109\/ICCAD.2015.7372576"},{"key":"e_1_3_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_2_1_4_1","volume-title":"International Symposium on Applied Reconfigurable Computing","author":"Arram J.","year":"2013"},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1145\/2746539.2746612"},{"key":"e_1_3_2_1_6_1","volume-title":"IEEE Workload Characterization Symposium","author":"Bader D.A.","year":"2005"},{"key":"e_1_3_2_1_7_1","volume-title":"ASAP: Accelerated Short-Read Alignment on Programmable Hardware","author":"Banerjee S.S.","year":"2018"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3406"},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg500"},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147"},{"key":"e_1_3_2_1_11_1","unstructured":"Design Compiler: https:\/\/www.synopsys.com\/implementation-and-signoff\/rtl-synthesis-test\/dc-ultra.html.  Design Compiler: https:\/\/www.synopsys.com\/implementation-and-signoff\/rtl-synthesis-test\/dc-ultra.html."},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1109\/TVLSI.2010.2049867"},{"key":"e_1_3_2_1_13_1","unstructured":"Farrar M.S. 2008. Optimizing Smith-Waterman for the Cell Broadband Engine. Bioinformatics. (2008).  Farrar M.S. 2008. Optimizing Smith-Waterman for the Cell Broadband Engine. Bioinformatics. (2008)."},{"key":"e_1_3_2_1_14_1","volume-title":"Proceedings of the 45nd Annual International Symposium on Computer Architecture - ISCA '18","author":"Fujiki D.","year":"2018"},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2015.0237"},{"key":"e_1_3_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2012.46.8934"},{"key":"e_1_3_2_1_17_1","unstructured":"GeForce GTX 1080 Specifications: https:\/\/www.geforce.com\/hardware\/desktop-gpus\/geforce-gtx-1080\/specifications.  GeForce GTX 1080 Specifications: https:\/\/www.geforce.com\/hardware\/desktop-gpus\/geforce-gtx-1080\/specifications."},{"key":"e_1_3_2_1_18_1","unstructured":"GeForce GTX TITAN X Specifications: https:\/\/www.geforce.com\/hardware\/desktop-gpus\/geforce-gtxtitan-x\/specifications.  GeForce GTX TITAN X Specifications: https:\/\/www.geforce.com\/hardware\/desktop-gpus\/geforce-gtxtitan-x\/specifications."},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90398-9"},{"key":"e_1_3_2_1_20_1","volume-title":"et al","author":"Harrow J.","year":"2012"},{"key":"e_1_3_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.22.10915"},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1109\/ISSCC.2014.6757323"},{"key":"e_1_3_2_1_23_1","volume-title":"Proceedings of the Asia and South Pacific Design Automation Conference, ASP-DAC. 298","author":"Hu M.","year":"2011"},{"key":"e_1_3_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2011.42"},{"key":"e_1_3_2_1_25_1","volume-title":"55th Annual Design Automation Conference","author":"Huangfu W.","year":"2018"},{"key":"e_1_3_2_1_26_1","unstructured":"Illumina Promises To Sequence Human Genome For $100 -- But Not Quite Yet: https:\/\/www.forbes.com\/sites\/matthewherper\/2017\/01\/09\/illumina-promises-to-sequence-human-genome-for-100-but-not-quite-yet.  Illumina Promises To Sequence Human Genome For $100 -- But Not Quite Yet: https:\/\/www.forbes.com\/sites\/matthewherper\/2017\/01\/09\/illumina-promises-to-sequence-human-genome-for-100-but-not-quite-yet."},{"key":"e_1_3_2_1_27_1","unstructured":"Intel\u00ae CoreTM i5-2520M Processor (3M Cache up to 3.20 GHz) Product Specifications: https:\/\/ark.intel.com\/products\/52229\/Intel-Core-i5-2520M-Processor-3M-Cache-up-to-3-20-GHz-.  Intel\u00ae CoreTM i5-2520M Processor (3M Cache up to 3.20 GHz) Product Specifications: https:\/\/ark.intel.com\/products\/52229\/Intel-Core-i5-2520M-Processor-3M-Cache-up-to-3-20-GHz-."},{"key":"e_1_3_2_1_28_1","unstructured":"Intel\u00ae Xeon\u00ae Processor E5-2670 (20M Cache 2.60 GHz 8.00 GT\/s Intel\u00ae QPI) Product Specifications: https:\/\/ark.intel.com\/products\/64595\/Intel-Xeon-Processor-E5-2670-20M-Cache-2-60-GHz-8-00-GT-s-Intel-QPI-.  Intel\u00ae Xeon\u00ae Processor E5-2670 (20M Cache 2.60 GHz 8.00 GT\/s Intel\u00ae QPI) Product Specifications: https:\/\/ark.intel.com\/products\/64595\/Intel-Xeon-Processor-E5-2670-20M-Cache-2-60-GHz-8-00-GT-s-Intel-QPI-."},{"key":"e_1_3_2_1_29_1","unstructured":"Intel\u00ae Xeon\u00ae Processor E5-2683 v4 (40M Cache 2.10 GHz) Product Specifications: https:\/\/ark.intel.com\/products\/91766\/Intel-Xeon-Processor-E5-2683-v4-40M-Cache-2-10-GHz-.  Intel\u00ae Xeon\u00ae Processor E5-2683 v4 (40M Cache 2.10 GHz) Product Specifications: https:\/\/ark.intel.com\/products\/91766\/Intel-Xeon-Processor-E5-2683-v4-40M-Cache-2-10-GHz-."},{"key":"e_1_3_2_1_30_1","unstructured":"Intel\u00ae Xeon PhiTM Processor 7250 (16GB 1.40 GHz 68 core) Product Specifications: https:\/\/ark.intel.com\/products\/94035\/Intel-Xeon-Phi-Processor-7250-16GB-1-40-GHz-68-core-.  Intel\u00ae Xeon PhiTM Processor 7250 (16GB 1.40 GHz 68 core) Product Specifications: https:\/\/ark.intel.com\/products\/94035\/Intel-Xeon-Phi-Processor-7250-16GB-1-40-GHz-68-core-."},{"key":"e_1_3_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1070"},{"key":"e_1_3_2_1_32_1","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2017.3211121"},{"key":"e_1_3_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/5.2.150"},{"key":"e_1_3_2_1_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-2-r12"},{"key":"e_1_3_2_1_35_1","volume-title":"SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. 2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS). (May 2017","author":"Lan H.","year":"2017"},{"key":"e_1_3_2_1_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbq015"},{"key":"e_1_3_2_1_37_1","doi-asserted-by":"publisher","DOI":"10.1109\/CLUSTER.2014.6968772"},{"key":"e_1_3_2_1_38_1","doi-asserted-by":"publisher","DOI":"10.1109\/TVLSI.2013.2277715"},{"key":"e_1_3_2_1_39_1","unstructured":"Maxeler Technologies: http:\/\/www.maxeler.com\/products\/.  Maxeler Technologies: http:\/\/www.maxeler.com\/products\/."},{"key":"e_1_3_2_1_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3043"},{"key":"e_1_3_2_1_41_1","volume-title":"Board Specification TESLA M2090 DUAL-SLOT COMPUTING PROCESSOR MODULE.","author":"NVIDIA","year":"2011"},{"key":"e_1_3_2_1_42_1","doi-asserted-by":"publisher","DOI":"10.1109\/JSSC.2005.864128"},{"key":"e_1_3_2_1_43_1","volume-title":"An introduction to sequence similarity (\"homology\") searching. Current Protocols in Bioinformatics","author":"Pearson W.R.","year":"2013"},{"key":"e_1_3_2_1_44_1","doi-asserted-by":"crossref","unstructured":"Ramirez A. Felipe Cabarcas Ben Juurlink Mesa M.A. Sanchez F. Azevedo A. Meenderinck C. Ciobanu C. Isaza S. and Gaydadjiev G. 2010. The SARC architecture. IEEE micro. 30 5 (2010) 16--29.  Ramirez A. Felipe Cabarcas Ben Juurlink Mesa M.A. Sanchez F. Azevedo A. Meenderinck C. Ciobanu C. Isaza S. and Gaydadjiev G. 2010. The SARC architecture. IEEE micro. 30 5 (2010) 16--29.","DOI":"10.1109\/MM.2010.79"},{"key":"e_1_3_2_1_45_1","doi-asserted-by":"publisher","DOI":"10.1001\/jamaneurol.2016.0301"},{"key":"e_1_3_2_1_46_1","first-page":"1","article-title":"Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins","volume":"9","author":"Sander C.","year":"1991","journal-title":"Structure, Function, and Genetics."},{"key":"e_1_3_2_1_47_1","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2016.2515597"},{"key":"e_1_3_2_1_48_1","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2008.4536328"},{"key":"e_1_3_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.1109\/TC.2009.133"},{"key":"e_1_3_2_1_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(81)90087-5"},{"key":"e_1_3_2_1_51_1","volume-title":"Big Data: Astronomical or Genomical? PLoS biology. 13, 7","author":"Stephens Z.D.","year":"2015"},{"key":"e_1_3_2_1_52_1","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-1-107"},{"key":"e_1_3_2_1_53_1","doi-asserted-by":"crossref","unstructured":"Torrezan A. Strachan J. Medeiros-Ribeiro G. and Williams R.S. 2011. Sub-nanosecond switching of a tantalum oxide memristor. Nanotechnology. 22 48 (2011).  Torrezan A. Strachan J. Medeiros-Ribeiro G. and Williams R.S. 2011. Sub-nanosecond switching of a tantalum oxide memristor. Nanotechnology. 22 48 (2011).","DOI":"10.1088\/0957-4484\/22\/48\/485203"},{"key":"e_1_3_2_1_54_1","doi-asserted-by":"publisher","DOI":"10.1145\/3173162.3173193"},{"key":"e_1_3_2_1_55_1","unstructured":"UniProt Knowledge Base: http:\/\/www.uniprot.org\/uniprot\/. Accessed: 2017-08-23.  UniProt Knowledge Base: http:\/\/www.uniprot.org\/uniprot\/. Accessed: 2017-08-23."},{"key":"e_1_3_2_1_56_1","first-page":"10","article-title":"Circuit Elements With Memory: Memristors, Memcapacitors, and Meminductors","volume":"97","author":"Di Ventra M.","year":"2009","journal-title":"Proceedings of the IEEE."},{"key":"e_1_3_2_1_57_1","volume-title":"The FPGA-Based High-Performance Computer RIVYERA for Applications in Bioinformatics. Conference on Computability in Europe","author":"Wienbrandt L.","year":"2014"},{"key":"e_1_3_2_1_58_1","doi-asserted-by":"publisher","DOI":"10.1109\/JPROC.2012.2190369"},{"key":"e_1_3_2_1_59_1","doi-asserted-by":"publisher","DOI":"10.1109\/LCA.2014.2374597"}],"event":{"name":"SYSTOR '20: The 13th ACM International Systems and Storage Conference","location":"Haifa Israel","acronym":"SYSTOR '20","sponsor":["Technion Israel Institute of Technology","SIGOPS ACM Special Interest Group on Operating Systems"]},"container-title":["Proceedings of the 13th ACM International Systems and Storage Conference"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3383669.3398279","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3383669.3398279","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T22:33:18Z","timestamp":1750199598000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3383669.3398279"}},"subtitle":["In-Memory Biological Sequence Alignment Accelerator for Large-Scale Genomic Data"],"short-title":[],"issued":{"date-parts":[[2020,5,30]]},"references-count":59,"alternative-id":["10.1145\/3383669.3398279","10.1145\/3383669"],"URL":"https:\/\/doi.org\/10.1145\/3383669.3398279","relation":{},"subject":[],"published":{"date-parts":[[2020,5,30]]},"assertion":[{"value":"2020-05-30","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}