{"id":"https://openalex.org/W2019176653","doi":"https://doi.org/10.1109/asap.2014.6868657","title":"SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors","display_name":"SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2019176653","doi":"https://doi.org/10.1109/asap.2014.6868657","mag":"2019176653"},"language":"en","primary_location":{"id":"doi:10.1109/asap.2014.6868657","is_oa":false,"landing_page_url":"https://doi.org/10.1109/asap.2014.6868657","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 25th International Conference on Application-Specific Systems, Architectures and Processors","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1404.4152","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yongchao Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yongchao Liu","raw_affiliation_strings":["Institut f\u00fcr Informatik Johannes Gutenberg Universit\u00e4t Mainz Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik Johannes Gutenberg Universit\u00e4t Mainz Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":null,"display_name":"Bertil Schmidt","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institut f\u00fcr Informatik Johannes Gutenberg Universit\u00e4t Mainz Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik Johannes Gutenberg Universit\u00e4t Mainz Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"184","last_page":"185"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9954000115394592,"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":0.9954000115394592,"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":0.9952999949455261,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.9192000031471252},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7057999968528748},{"id":"https://openalex.org/keywords/coprocessor","display_name":"Coprocessor","score":0.6898999810218811},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.5527999997138977},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.5418000221252441},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.4609000086784363}],"concepts":[{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.9192000031471252},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7556999921798706},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7077000141143799},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7057999968528748},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.6898999810218811},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.5527999997138977},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.5418000221252441},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.4609000086784363},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.43290001153945923},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38109999895095825},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.3774000108242035},{"id":"https://openalex.org/C64270927","wikidata":"https://www.wikidata.org/wiki/Q206924","display_name":"PCI Express","level":3,"score":0.3756999969482422},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.3635999858379364},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.2583000063896179}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/asap.2014.6868657","is_oa":false,"landing_page_url":"https://doi.org/10.1109/asap.2014.6868657","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 25th International Conference on Application-Specific Systems, Architectures and Processors","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1404.4152","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1404.4152","pdf_url":"https://arxiv.org/pdf/1404.4152","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1404.4152","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1404.4152","pdf_url":"https://arxiv.org/pdf/1404.4152","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2015915218","https://openalex.org/W2065461987","https://openalex.org/W2087064593","https://openalex.org/W2142678478","https://openalex.org/W2146379626","https://openalex.org/W6685248075"],"related_works":[],"abstract_inverted_index":{"The":[0],"maximal":[1],"sensitivity":[2,20],"of":[3,25,113,162],"the":[4,18,23,31,44,49,64,76,80,86,104,159],"Smith-Waterman":[5,55],"algorithm":[6,32,47],"has":[7],"enabled":[8],"its":[9],"wide":[10,91],"use":[11],"in":[12],"biological":[13],"sequence":[14],"database":[15,57],"search.":[16,58],"Unfortunately,":[17],"high":[19],"comes":[21],"at":[22,171],"expense":[24],"quadratic":[26],"time":[27],"complexity,":[28],"which":[29],"makes":[30],"computationally":[33],"demanding":[34],"for":[35],"big":[36],"databases.":[37],"In":[38],"this":[39],"paper,":[40],"we":[41],"present":[42],"SWAPHI,":[43],"first":[45],"parallelized":[46],"employing":[48],"emerging":[50],"Xeon":[51,126,135,141],"Phis":[52,142],"to":[53,115,130,145],"accelerate":[54],"protein":[56,107],"SWAPHI":[59,109,138,167],"is":[60,143,168],"designed":[61],"based":[62],"on":[63,123,133,148,155],"scale-and-vectorize":[65],"approach,":[66],"i.e.":[67],"it":[68],"boosts":[69],"alignment":[70],"speed":[71],"by":[72],"effectively":[73],"utilizing":[74],"both":[75,146],"coarse-grained":[77],"parallelism":[78,88],"from":[79,89],"many":[81],"co-processing":[82],"cores":[83,152],"(scale)":[84],"and":[85,128,153,164],"fine-grained":[87],"512-bit":[90],"single":[92,125],"instruction":[93],"multiple":[94],"data":[95],"(SIMD)":[96],"vectors":[97],"per":[98,120],"core":[99],"(vectorize).":[100],"By":[101],"searching":[102],"against":[103],"large":[105],"UniProtKB/TrEMBL":[106],"database,":[108],"achieves":[110],"a":[111,124],"performance":[112],"up":[114,129],"58.8":[116],"billion":[117],"cell":[118],"updates":[119],"second":[121],"(GCUPS)":[122],"Phi":[127],"228.4":[131],"GCUPS":[132],"four":[134,140],"Phis.":[136],"Moreover,":[137],"using":[139],"superior":[144],"SWIPE":[147],"16":[149],"highend":[150],"CPU":[151],"BLAST+":[154],"8":[156],"cores,":[157],"with":[158],"maximum":[160],"speedup":[161],"1.52":[163],"1.86,":[165],"respectively.":[166],"freely":[169],"available":[170],"http://swaphi.sourceforge.net.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2016-06-24T00:00:00"}
