{"id":"https://openalex.org/W2065461987","doi":"https://doi.org/10.1186/1471-2105-14-117","title":"CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions","display_name":"CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions","publication_year":2013,"publication_date":"2013-04-04","ids":{"openalex":"https://openalex.org/W2065461987","doi":"https://doi.org/10.1186/1471-2105-14-117","mag":"2065461987","pmid":"https://pubmed.ncbi.nlm.nih.gov/23557111"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-117","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-117","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-117","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100617992","display_name":"Yongchao Liu","orcid":"https://orcid.org/0000-0003-3440-9675"},"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":true,"raw_author_name":"Yongchao Liu","raw_affiliation_strings":["Institut f\u00fcr Informatik, Johannes Gutenberg Universit\u00e4t Mainz, Mainz, Germany. liuy@uni-mainz.de","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. liuy@uni-mainz.de","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institut f\u00fcr Informatik, Johannes Gutenberg Universit\u00e4t Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074813540","display_name":"Adrianto Wirawan","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":"Adrianto Wirawan","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":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"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":true,"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":["https://openalex.org/A5020388832","https://openalex.org/A5100617992"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1545,"currency":"EUR","value_usd":1666},"fwci":13.2066,"has_fulltext":true,"cited_by_count":233,"citation_normalized_percentile":{"value":0.99322107,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"14","issue":"1","first_page":"117","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.42669999599456787,"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":0.42669999599456787,"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":0.17190000414848328,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.06870000064373016,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/simd","display_name":"SIMD","score":0.914656400680542},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8780015110969543},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7959865927696228},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7440803647041321},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.7132090330123901},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.4568948745727539},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4410724639892578},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1587229073047638},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.09919923543930054}],"concepts":[{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.914656400680542},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8780015110969543},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7959865927696228},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7440803647041321},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.7132090330123901},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.4568948745727539},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4410724639892578},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1587229073047638},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.09919923543930054},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-14-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-117","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-117","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23557111","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23557111","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2643381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3637623","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-117","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-117","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065461987.pdf","grobid_xml":"https://content.openalex.org/works/W2065461987.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W2006899413","https://openalex.org/W2011652244","https://openalex.org/W2013733655","https://openalex.org/W2015292449","https://openalex.org/W2015915218","https://openalex.org/W2019649531","https://openalex.org/W2036880373","https://openalex.org/W2044338118","https://openalex.org/W2055043387","https://openalex.org/W2068448872","https://openalex.org/W2068659823","https://openalex.org/W2087064593","https://openalex.org/W2099084006","https://openalex.org/W2103441770","https://openalex.org/W2106882534","https://openalex.org/W2107824361","https://openalex.org/W2116508956","https://openalex.org/W2117683095","https://openalex.org/W2118874283","https://openalex.org/W2122942724","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2133540884","https://openalex.org/W2140858267","https://openalex.org/W2141697594","https://openalex.org/W2142667471","https://openalex.org/W2142678478","https://openalex.org/W2146379626","https://openalex.org/W2155503253","https://openalex.org/W2158714788","https://openalex.org/W2160097763","https://openalex.org/W2165949232","https://openalex.org/W2166081493","https://openalex.org/W2166760518","https://openalex.org/W2170896626","https://openalex.org/W2184753910","https://openalex.org/W2269349250","https://openalex.org/W4251237680"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W1912958759","https://openalex.org/W2792081825"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,245],"maximal":[2],"sensitivity":[3],"for":[4,14,93],"local":[5],"alignments":[6],"makes":[7],"the":[8,24,40,74,87,94,114,137,211,227,238,249],"Smith-Waterman":[9,53],"algorithm":[10,25,78,183,215],"a":[11,30,51,97,145,157,166,172],"popular":[12],"choice":[13],"protein":[15,54],"sequence":[16,44,119],"database":[17,55,139],"search":[18,56],"based":[19,129,209],"on":[20,130,136,165,210,241],"pairwise":[21],"alignment.":[22],"However,":[23],"is":[26,198],"compute-intensive":[27],"due":[28],"to":[29,108,152],"quadratic":[31],"time":[32,96],"complexity.":[33],"Corresponding":[34],"runtimes":[35],"are":[36,122,252],"further":[37],"compounded":[38],"by":[39,224],"rapid":[41],"growth":[42],"of":[43,160,229],"databases.":[45],"RESULTS:":[46],"We":[47],"present":[48],"CUDASW++":[49,142,149,196,222],"3.0,":[50],"fast":[52],"algorithm,":[57],"which":[58,101],"couples":[59],"CPU":[60,69,75,230],"and":[61,65,70,127,154,162,171,193,203,231,243,248],"GPU":[62,71,88,98,232],"SIMD":[63,99,105,233],"instructions":[64,107,234],"carries":[66],"out":[67],"concurrent":[68,239],"computations.":[72],"For":[73,86],"computation,":[76,89],"this":[77],"employs":[79,102],"SSE-based":[80],"vector":[81],"execution":[82,116,240],"units":[83],"as":[84,235,237],"accelerators.":[85],"we":[90],"have":[91],"investigated":[92],"first":[95],"parallelization,":[100],"CUDA":[103,201],"PTX":[104,204],"video":[106],"gain":[109],"more":[110],"data":[111,251],"parallelism":[112],"beyond":[113],"SIMT":[115],"model.":[117],"Moreover,":[118],"alignment":[120],"workloads":[121],"automatically":[123],"distributed":[124],"over":[125,148,188,219],"CPUs":[126,242],"GPUs":[128,208],"their":[131],"respective":[132],"compute":[133],"capabilities.":[134],"Evaluation":[135],"Swiss-Prot":[138],"shows":[140],"that":[141],"3.0":[143,197],"gains":[144],"performance":[146,159],"improvement":[147],"2.0":[150],"up":[151],"2.9":[153],"3.2,":[155],"with":[156],"maximum":[158],"119.0":[161],"185.6":[163],"GCUPS,":[164],"single-GPU":[167],"GeForce":[168,174],"GTX":[169,175],"680":[170],"dual-GPU":[173],"690":[176],"graphics":[177],"card,":[178],"respectively.":[179],"In":[180],"addition,":[181],"our":[182],"has":[184],"demonstrated":[185],"significant":[186,217],"speedups":[187,218],"other":[189],"top-performing":[190],"tools:":[191],"SWIPE":[192],"BLAST+.":[194],"CONCLUSIONS:":[195],"written":[199],"in":[200],"C++":[202],"assembly":[205],"languages,":[206],"targeting":[207],"Kepler":[212],"architecture.":[213],"This":[214],"obtains":[216],"its":[220],"predecessor:":[221],"2.0,":[223],"benefiting":[225],"from":[226],"use":[228],"well":[236],"GPUs.":[244],"source":[246],"code":[247],"simulated":[250],"available":[253],"at":[254],"http://cudasw.sourceforge.net.":[255]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":35},{"year":2015,"cited_by_count":28},{"year":2014,"cited_by_count":27},{"year":2013,"cited_by_count":6}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
