{"id":"https://openalex.org/W2052792878","doi":"https://doi.org/10.1109/cluster.2014.6968784","title":"Smith-Waterman algorithm on heterogeneous systems: A case study","display_name":"Smith-Waterman algorithm on heterogeneous systems: A case study","publication_year":2014,"publication_date":"2014-09-01","ids":{"openalex":"https://openalex.org/W2052792878","doi":"https://doi.org/10.1109/cluster.2014.6968784","mag":"2052792878"},"language":"en","primary_location":{"id":"doi:10.1109/cluster.2014.6968784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cluster.2014.6968784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Cluster Computing (CLUSTER)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://sedici.unlp.edu.ar/handle/10915/82886","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065094174","display_name":"Enzo Rucci","orcid":"https://orcid.org/0000-0001-6736-7358"},"institutions":[{"id":"https://openalex.org/I874386039","display_name":"Universidad Nacional de La Plata","ror":"https://ror.org/01tjs6929","country_code":"AR","type":"education","lineage":["https://openalex.org/I874386039"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Enzo Rucci","raw_affiliation_strings":["Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]},{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101621664","display_name":"Armando De Giusti","orcid":"https://orcid.org/0000-0002-6459-3592"},"institutions":[{"id":"https://openalex.org/I874386039","display_name":"Universidad Nacional de La Plata","ror":"https://ror.org/01tjs6929","country_code":"AR","type":"education","lineage":["https://openalex.org/I874386039"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Armando De Giusti","raw_affiliation_strings":["Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]},{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084392593","display_name":"Marcelo Naiouf","orcid":"https://orcid.org/0000-0001-9127-3212"},"institutions":[{"id":"https://openalex.org/I874386039","display_name":"Universidad Nacional de La Plata","ror":"https://ror.org/01tjs6929","country_code":"AR","type":"education","lineage":["https://openalex.org/I874386039"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Marcelo Naiouf","raw_affiliation_strings":["Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata La Plata (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]},{"raw_affiliation_string":"Instituto de Investigacion en Informatica LIDI (III-LIDI), Universidad Nacional de La Plata, (1900), Buenos Aires, Argentina","institution_ids":["https://openalex.org/I874386039"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040019079","display_name":"Guillermo Botella","orcid":"https://orcid.org/0000-0002-0848-2636"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Guillermo Botella","raw_affiliation_strings":["Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048493144","display_name":"Carlos Garc\u00eda","orcid":"https://orcid.org/0000-0002-3470-1097"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Garcia","raw_affiliation_strings":["Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047526101","display_name":"Manuel Prieto","orcid":"https://orcid.org/0000-0003-0687-3737"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Manuel Prieto-Matias","raw_affiliation_strings":["Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Dept. Computer Architecture, Complutense University of Madrid, 28040, Spain","institution_ids":["https://openalex.org/I121748325"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":12.1143,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.98550517,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"323","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996399998664856,"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":0.996399998664856,"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":0.9702000021934509,"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/computer-science","display_name":"Computer science","score":0.8376832008361816},{"id":"https://openalex.org/keywords/coprocessor","display_name":"Coprocessor","score":0.8159327507019043},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.780846118927002},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7679428458213806},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.7642475366592407},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.713689923286438},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.649219274520874},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.563287615776062},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.5076414346694946},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.500438928604126},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4927871525287628},{"id":"https://openalex.org/keywords/symmetric-multiprocessor-system","display_name":"Symmetric multiprocessor system","score":0.45770809054374695},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18141868710517883}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8376832008361816},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.8159327507019043},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.780846118927002},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7679428458213806},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.7642475366592407},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.713689923286438},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.649219274520874},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.563287615776062},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.5076414346694946},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.500438928604126},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4927871525287628},{"id":"https://openalex.org/C172430144","wikidata":"https://www.wikidata.org/wiki/Q17111997","display_name":"Symmetric multiprocessor system","level":2,"score":0.45770809054374695},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18141868710517883},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/cluster.2014.6968784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cluster.2014.6968784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Cluster Computing (CLUSTER)","raw_type":"proceedings-article"},{"id":"pmh:oai:sedici.unlp.edu.ar:10915/82886","is_oa":true,"landing_page_url":"http://sedici.unlp.edu.ar/handle/10915/82886","pdf_url":null,"source":{"id":"https://openalex.org/S4306400803","display_name":"El Servicio de Difusi\u00f3n de la Creaci\u00f3n Intelectual (National University of La Plata)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I874386039","host_organization_name":"Universidad Nacional de La Plata","host_organization_lineage":["https://openalex.org/I874386039"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Objeto de conferencia"}],"best_oa_location":{"id":"pmh:oai:sedici.unlp.edu.ar:10915/82886","is_oa":true,"landing_page_url":"http://sedici.unlp.edu.ar/handle/10915/82886","pdf_url":null,"source":{"id":"https://openalex.org/S4306400803","display_name":"El Servicio de Difusi\u00f3n de la Creaci\u00f3n Intelectual (National University of La Plata)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I874386039","host_organization_name":"Universidad Nacional de La Plata","host_organization_lineage":["https://openalex.org/I874386039"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Objeto de conferencia"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321594","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1244930767","https://openalex.org/W1566539040","https://openalex.org/W1572872217","https://openalex.org/W1573897044","https://openalex.org/W1607038151","https://openalex.org/W1990800384","https://openalex.org/W2006899413","https://openalex.org/W2015915218","https://openalex.org/W2019176653","https://openalex.org/W2036880373","https://openalex.org/W2055043387","https://openalex.org/W2065461987","https://openalex.org/W2068659823","https://openalex.org/W2093931624","https://openalex.org/W2117683095","https://openalex.org/W2133540884","https://openalex.org/W2146379626","https://openalex.org/W2158714788","https://openalex.org/W2608060838","https://openalex.org/W3105244973","https://openalex.org/W4236236547","https://openalex.org/W4285719527","https://openalex.org/W6634012511"],"related_works":["https://openalex.org/W2213533160","https://openalex.org/W4252450863","https://openalex.org/W2467043670","https://openalex.org/W2022867993","https://openalex.org/W2085105049","https://openalex.org/W3203561460","https://openalex.org/W3009624197","https://openalex.org/W4251138667","https://openalex.org/W2682544458","https://openalex.org/W1586106326"],"abstract_inverted_index":{"The":[0],"well-known":[1,89],"Smith-Waterman":[2],"(SW)":[3],"algorithm":[4],"is":[5,14,103],"a":[6,75,93,98],"high-sensitivity":[7],"method":[8],"for":[9],"local":[10],"alignments.":[11],"However,":[12],"SW":[13,61,72],"expensive":[15],"in":[16,29],"terms":[17],"of":[18,40],"both":[19],"execution":[20],"time":[21],"and":[22,55,62],"memory":[23],"usage,":[24],"which":[25],"makes":[26],"it":[27],"impractical":[28],"many":[30],"applications.":[31],"Some":[32],"heuristics":[33],"are":[34,57],"possible":[35],"but":[36],"at":[37],"the":[38,88],"expense":[39],"losing":[41],"sensitivity.":[42],"Fortunately,":[43],"previous":[44],"research":[45],"have":[46,70],"shown":[47,96],"that":[48,97],"new":[49],"computing":[50],"platforms":[51],"such":[52],"as":[53,92],"GPUs":[54],"FPGAs":[56],"able":[58,104],"to":[59,105],"accelerate":[60],"achieve":[63,106],"impressive":[64],"speedups.":[65],"In":[66],"this":[67],"paper":[68],"we":[69],"explored":[71],"acceleration":[73],"on":[74],"heterogeneous":[76,101],"platform":[77],"equipped":[78],"with":[79,112],"an":[80],"Intel":[81],"Xeon":[82],"Phi":[83],"coprocessor.":[84],"Our":[85],"evaluation,":[86],"using":[87],"Swiss-Prot":[90],"database":[91],"benchmark,":[94],"has":[95],"hybrid":[99],"CPU-Phi":[100],"system":[102],"competitive":[107],"performance":[108],"(62.6":[109],"GCUPS),":[110],"even":[111],"moderate":[113],"low-level":[114],"optimisations.":[115]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
