{"id":"https://openalex.org/W4385679804","doi":"https://doi.org/10.1109/iscas46773.2023.10181600","title":"On the Genome Sequence Alignment FPGA Acceleration via KSW2z","display_name":"On the Genome Sequence Alignment FPGA Acceleration via KSW2z","publication_year":2023,"publication_date":"2023-05-21","ids":{"openalex":"https://openalex.org/W4385679804","doi":"https://doi.org/10.1109/iscas46773.2023.10181600"},"language":"en","primary_location":{"id":"doi:10.1109/iscas46773.2023.10181600","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iscas46773.2023.10181600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Symposium on Circuits and Systems (ISCAS)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005739756","display_name":"Alberto Zeni","orcid":"https://orcid.org/0000-0003-4005-6036"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alberto Zeni","raw_affiliation_strings":["Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063408697","display_name":"Guido Walter Di Donato","orcid":"https://orcid.org/0000-0003-2026-9755"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Guido Walter Di Donato","raw_affiliation_strings":["Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109629142","display_name":"Alessia Della Valle","orcid":null},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessia Della Valle","raw_affiliation_strings":["Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066330654","display_name":"Filippo Carloni","orcid":"https://orcid.org/0000-0001-7084-7184"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Filippo Carloni","raw_affiliation_strings":["Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010543929","display_name":"Marco D. Santambrogio","orcid":"https://orcid.org/0000-0002-9883-9693"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco D. Santambrogio","raw_affiliation_strings":["Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Politecnico di Milano,Informatica e Bioingegneria,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informatica e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9799000024795532,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6719311475753784},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6543744206428528},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5603447556495667},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.5161862969398499},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5109307169914246},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.5106795430183411},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.4975147545337677},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4882371723651886},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4859656095504761},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.4820995628833771},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.479801207780838},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.45869866013526917},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41049572825431824},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32485654950141907},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.2792373299598694},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.22133177518844604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2102968394756317},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13803967833518982},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0837295651435852}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6719311475753784},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6543744206428528},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5603447556495667},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.5161862969398499},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5109307169914246},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.5106795430183411},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.4975147545337677},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4882371723651886},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4859656095504761},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.4820995628833771},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.479801207780838},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.45869866013526917},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41049572825431824},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32485654950141907},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2792373299598694},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.22133177518844604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2102968394756317},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13803967833518982},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0837295651435852},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/iscas46773.2023.10181600","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iscas46773.2023.10181600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Symposium on Circuits and Systems (ISCAS)","raw_type":"proceedings-article"},{"id":"pmh:oai:re.public.polimi.it:11311/1248219","is_oa":false,"landing_page_url":"https://hdl.handle.net/11311/1248219","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W2006899413","https://openalex.org/W2011218124","https://openalex.org/W2021342241","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2107986228","https://openalex.org/W2132967231","https://openalex.org/W2134800079","https://openalex.org/W2142678478","https://openalex.org/W2158714788","https://openalex.org/W2170551349","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2912320302","https://openalex.org/W3042377559","https://openalex.org/W3167680374","https://openalex.org/W3176565954","https://openalex.org/W3186590823","https://openalex.org/W4254502766","https://openalex.org/W4294733767","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6799309275","https://openalex.org/W6842803579"],"related_works":["https://openalex.org/W947442053","https://openalex.org/W2766664604","https://openalex.org/W2214459866","https://openalex.org/W1985609517","https://openalex.org/W1639707418","https://openalex.org/W2475524688","https://openalex.org/W2074831258","https://openalex.org/W3105244973","https://openalex.org/W2981619930","https://openalex.org/W2166164399"],"abstract_inverted_index":{"Pairwise":[0],"sequence":[1],"alignment":[2,20,79],"is":[3],"a":[4,120],"fundamental":[5],"step":[6],"for":[7],"many":[8],"genomics":[9],"and":[10,27,77,105],"molecular":[11],"biology":[12],"applications.":[13],"Given":[14],"the":[15,22,38,43,54,60,71,81,87,114],"quadratic":[16],"time":[17,89],"complexity":[18],"of":[19,46,59],"algorithms,":[21],"community":[23],"demands":[24],"innovative,":[25],"fast,":[26],"efficient":[28],"techniques":[29],"to":[30,41,84,98,113],"perform":[31],"this":[32,50],"task.":[33],"Furthermore,":[34],"general-purpose":[35],"architectures":[36],"lack":[37],"necessary":[39],"performance":[40],"address":[42],"computational":[44],"load":[45],"these":[47],"algorithms.":[48],"In":[49],"context,":[51],"we":[52],"present":[53],"first":[55],"open-source":[56],"FPGA":[57],"implementation":[58,117],"popular":[61],"KSW2z":[62],"algorithm":[63],"employed":[64],"by":[65],"minimap2.":[66],"Our":[67],"design":[68],"also":[69],"implements":[70],"<tex":[72,99,106],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[73,100,107],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$Z-":[74],"\\mathbf{drop}$</tex>":[75],"heuristic":[76],"banded":[78],"as":[80],"original":[82],"software":[83,116],"further":[85],"reduce":[86],"processing":[88],"if":[90],"needed.":[91],"The":[92],"proposed":[93],"multi-core":[94],"accelerator":[95],"achieves":[96],"up":[97],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\mathbf{7.70}\\times$</tex>":[101],"improvement":[102],"in":[103,109],"speedup":[104],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\mathbf{20.07}\\times$</tex>":[108],"energy":[110],"efficiency":[111],"compared":[112],"multi-threaded":[115],"run":[118],"on":[119],"Xeon":[121],"Platinum":[122],"8167M":[123],"processor.":[124]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
