{"id":"https://openalex.org/W2165949232","doi":"https://doi.org/10.1109/ipdps.2009.5160931","title":"An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases","display_name":"An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases","publication_year":2009,"publication_date":"2009-05-01","ids":{"openalex":"https://openalex.org/W2165949232","doi":"https://doi.org/10.1109/ipdps.2009.5160931","mag":"2165949232"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2009.5160931","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2009.5160931","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Parallel &amp; Distributed Processing","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/A5006801741","display_name":"\u0141ukasz Ligowski","orcid":null},"institutions":[{"id":"https://openalex.org/I47996466","display_name":"University of Warmia and Mazury in Olsztyn","ror":"https://ror.org/05s4feg49","country_code":"PL","type":"education","lineage":["https://openalex.org/I47996466"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Lukasz Ligowski","raw_affiliation_strings":["Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warmia and Mazury, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warmia and Mazury, Warsaw, Poland","institution_ids":["https://openalex.org/I47996466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065166985","display_name":"Witold R. Rudnicki","orcid":"https://orcid.org/0000-0002-7928-4944"},"institutions":[{"id":"https://openalex.org/I47996466","display_name":"University of Warmia and Mazury in Olsztyn","ror":"https://ror.org/05s4feg49","country_code":"PL","type":"education","lineage":["https://openalex.org/I47996466"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Witold Rudnicki","raw_affiliation_strings":["Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warmia and Mazury, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warmia and Mazury, Warsaw, Poland","institution_ids":["https://openalex.org/I47996466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I47996466"],"apc_list":null,"apc_paid":null,"fwci":53.9869,"has_fulltext":false,"cited_by_count":157,"citation_normalized_percentile":{"value":0.99887149,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9973000288009644,"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":0.9876000285148621,"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/cuda","display_name":"CUDA","score":0.9018830060958862},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8373035192489624},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.8334842920303345},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7890341877937317},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.7180379033088684},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5775495767593384},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5642185211181641},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.5543107390403748},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5201247334480286},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4594486653804779},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.44753432273864746},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.4223189651966095},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3628677725791931},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.35531818866729736},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.2933518886566162},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.21592643857002258}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.9018830060958862},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8373035192489624},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.8334842920303345},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7890341877937317},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.7180379033088684},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5775495767593384},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5642185211181641},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.5543107390403748},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5201247334480286},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4594486653804779},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.44753432273864746},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.4223189651966095},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3628677725791931},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.35531818866729736},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2933518886566162},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.21592643857002258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/ipdps.2009.5160931","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2009.5160931","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Parallel &amp; Distributed Processing","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.157.939","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.157.939","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.hicomb.org/papers/HICOMB2009-10.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1546231652","https://openalex.org/W1977746661","https://openalex.org/W2009036829","https://openalex.org/W2011652244","https://openalex.org/W2011945323","https://openalex.org/W2015292449","https://openalex.org/W2043282445","https://openalex.org/W2055043387","https://openalex.org/W2069215288","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2096320147","https://openalex.org/W2108238461","https://openalex.org/W2121082877","https://openalex.org/W2128114769","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2140640076","https://openalex.org/W2141697594","https://openalex.org/W2143210482","https://openalex.org/W2146379626","https://openalex.org/W2147667050","https://openalex.org/W2149788502","https://openalex.org/W2158714788","https://openalex.org/W2160097763","https://openalex.org/W2166325055","https://openalex.org/W2166621589","https://openalex.org/W2616754551","https://openalex.org/W4236236547","https://openalex.org/W4246285230","https://openalex.org/W6632671545","https://openalex.org/W6674514985","https://openalex.org/W6680740241","https://openalex.org/W6682590169"],"related_works":["https://openalex.org/W2151046618","https://openalex.org/W1972148443","https://openalex.org/W1969233021","https://openalex.org/W2167646277","https://openalex.org/W2063573318","https://openalex.org/W1991259050","https://openalex.org/W2388314963","https://openalex.org/W3158047141","https://openalex.org/W1656096860","https://openalex.org/W2375309128"],"abstract_inverted_index":{"The":[0,27,93,123],"Smith":[1,86,110],"Waterman":[2,87,111],"algorithm":[3,88,94,112],"for":[4,18,35,58,135],"sequence":[5,19],"alignment":[6,23],"is":[7,16],"one":[8],"of":[9,13,24,46,51,84,108,119],"the":[10,85,90,109,133],"main":[11],"tools":[12],"bioinformatics.":[14],"It":[15],"used":[17,34],"similarity":[20],"searches":[21],"and":[22,70,127],"similar":[25],"sequences.":[26],"high":[28],"end":[29],"Graphical":[30],"Processing":[31],"Unit":[32],"(GPU),":[33],"processing":[36],"graphics":[37],"on":[38,67,75,89,113,139],"desktop":[39],"computers,":[40],"deliver":[41],"computational":[42],"capabilities":[43,55],"exceeding":[44],"those":[45],"CPUs":[47],"by":[48],"an":[49,81],"order":[50],"magnitude.":[52],"Recently":[53],"these":[54],"became":[56],"accessible":[57],"general":[59],"purpose":[60],"computations":[61],"thanks":[62],"to":[63],"CUDA":[64],"programming":[65],"environment":[66,74],"Nvidia":[68,91],"GPUs":[69],"ATI":[71,76],"Stream":[72],"Computing":[73],"GPUs.":[77],"Here":[78],"we":[79],"present":[80],"efficient":[82,137],"implementation":[83,107],"GPU.":[92,140],"achieves":[95],"more":[96,116],"than":[97,104,117],"3.5":[98],"times":[99],"higher":[100],"per":[101],"core":[102],"performance":[103],"previously":[105],"published":[106],"GPU,":[114],"reaching":[115],"70%":[118],"theoretical":[120],"hardware":[121],"performance.":[122],"differences":[124],"between":[125],"current":[126],"earlier":[128],"approaches":[129],"are":[130],"described":[131],"showing":[132],"example":[134],"writing":[136],"code":[138]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":20},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":22}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
