{"id":"https://openalex.org/W1989364947","doi":"https://doi.org/10.1109/ipdpsw.2010.5470748","title":"Fast Smith-Waterman hardware implementation","display_name":"Fast Smith-Waterman hardware implementation","publication_year":2010,"publication_date":"2010-04-01","ids":{"openalex":"https://openalex.org/W1989364947","doi":"https://doi.org/10.1109/ipdpsw.2010.5470748","mag":"1989364947"},"language":"en","primary_location":{"id":"doi:10.1109/ipdpsw.2010.5470748","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw.2010.5470748","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Symposium on Parallel &amp; Distributed Processing, Workshops and Phd Forum (IPDPSW)","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/A5101983834","display_name":"Zubair Nawaz","orcid":"https://orcid.org/0000-0002-7989-8401"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Zubair Nawaz","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technnology, Netherlands","Computer Engineering Lab., Delft University of Technology, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technnology, Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Computer Engineering Lab., Delft University of Technology, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058128591","display_name":"Koen Bertels","orcid":"https://orcid.org/0000-0001-9310-4885"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Koen Bertels","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technnology, Netherlands","Computer Engineering Lab., Delft University of Technology, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technnology, Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Computer Engineering Lab., Delft University of Technology, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003823095","display_name":"H. Ekin Sumbul","orcid":"https://orcid.org/0000-0001-6812-8033"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"H. Ekin Sumbul","raw_affiliation_strings":["Sabanci University, Turkey","Electronic Engineering Program, Sabanci University, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sabanci University, Turkey","institution_ids":["https://openalex.org/I134235054"]},{"raw_affiliation_string":"Electronic Engineering Program, Sabanci University, Turkey","institution_ids":["https://openalex.org/I134235054"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":7.3889,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.97467057,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9969000220298767,"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/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.9395999908447266,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dataflow","display_name":"Dataflow","score":0.9687633514404297},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8883339166641235},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8061665892601013},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7723450660705566},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.7072617411613464},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.616773784160614},{"id":"https://openalex.org/keywords/variable","display_name":"Variable (mathematics)","score":0.5183642506599426},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35099685192108154},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1431032419204712},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11550891399383545}],"concepts":[{"id":"https://openalex.org/C96324660","wikidata":"https://www.wikidata.org/wiki/Q205446","display_name":"Dataflow","level":2,"score":0.9687633514404297},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8883339166641235},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8061665892601013},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7723450660705566},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.7072617411613464},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.616773784160614},{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.5183642506599426},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35099685192108154},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1431032419204712},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11550891399383545},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/ipdpsw.2010.5470748","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw.2010.5470748","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Symposium on Parallel &amp; Distributed Processing, Workshops and Phd Forum (IPDPSW)","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.212.9837","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.212.9837","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://ce.et.tudelft.nl/publicationfiles/1827_689_IPDPS2010_camera_ready.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W121571527","https://openalex.org/W1566539040","https://openalex.org/W2039693716","https://openalex.org/W2045575721","https://openalex.org/W2068448872","https://openalex.org/W2119406408","https://openalex.org/W2122942724","https://openalex.org/W2142599417","https://openalex.org/W2163803863","https://openalex.org/W2543158077","https://openalex.org/W6605010064","https://openalex.org/W6634012511","https://openalex.org/W6681246114"],"related_works":["https://openalex.org/W2187181201","https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W4287182096","https://openalex.org/W1980160788"],"abstract_inverted_index":{"The":[0],"Smith-Waterman":[1],"(SW)":[2],"algorithm":[3],"is":[4,26,74],"one":[5],"of":[6,21,34,64,81],"the":[7,18,22,62,79],"widely":[8],"used":[9],"algorithms":[10],"for":[11,30],"sequence":[12,23],"alignment":[13],"in":[14],"computational":[15],"biology.":[16],"With":[17],"growing":[19],"size":[20],"database,":[24],"there":[25],"always":[27],"a":[28],"need":[29],"even":[31],"faster":[32,77],"implementation":[33,73],"SW.":[35],"In":[36],"this":[37],"paper,":[38],"we":[39],"have":[40],"implemented":[41],"two":[42],"Recursive":[43],"Variable":[44],"Expansion":[45],"(RVE)":[46],"based":[47],"techniques,":[48],"which":[49],"are":[50],"proved":[51],"to":[52,68],"give":[53],"better":[54],"speedup":[55],"than":[56],"any":[57],"best":[58],"dataflow":[59,69],"approach":[60],"at":[61,78],"cost":[63],"extra":[65],"area.":[66,85],"Compared":[67],"approach,":[70],"our":[71],"HW":[72],"2.29":[75],"times":[76,83],"expense":[80],"2.82":[82],"more":[84]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
