{"id":"https://openalex.org/W4205568950","doi":"https://doi.org/10.1109/date.2010.5457169","title":"A HMMER hardware accelerator using divergences","display_name":"A HMMER hardware accelerator using divergences","publication_year":2010,"publication_date":"2010-03-01","ids":{"openalex":"https://openalex.org/W4205568950","doi":"https://doi.org/10.1109/date.2010.5457169"},"language":"en","primary_location":{"id":"doi:10.1109/date.2010.5457169","is_oa":false,"landing_page_url":"https://doi.org/10.1109/date.2010.5457169","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 Design, Automation &amp; Test in Europe Conference &amp; Exhibition (DATE 2010)","raw_type":"proceedings-article"},"type":"article","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/A5049683710","display_name":"Juan Fernando Eusse Giraldo","orcid":null},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Juan Fernando Eusse Giraldo","raw_affiliation_strings":["Department of Electrical Engineering, University of Brasilia, DF, Brazil","Department of Electrical Engineering, University of Brasilia, Brasilia, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Brasilia, DF, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Department of Electrical Engineering, University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070434727","display_name":"Nahri Moreano","orcid":null},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Nahri Moreano","raw_affiliation_strings":["School of Computing, University of Mato Grosso do Sul, Campo Grande/MS, Brazil","School of Computing, University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of Mato Grosso do Sul, Campo Grande/MS, Brazil","institution_ids":["https://openalex.org/I122558511"]},{"raw_affiliation_string":"School of Computing, University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019378528","display_name":"Ricardo Pezzuol Jacobi","orcid":null},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ricardo Pezzuol Jacobi","raw_affiliation_strings":["Department of Computer Science, University of Brasilia, DF, Brazil","Department of Computer Science, University of Brasilia, Brasilia, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, DF, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005717412","display_name":"Alba Cristina Magalh\u00e3es Alves de Melo","orcid":null},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alba Cristina Magalhaes Alves de Melo","raw_affiliation_strings":["Department of Computer Science, University of Brasilia, DF, Brazil","Department of Computer Science, University of Brasilia, Brasilia, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, DF, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049683710"],"corresponding_institution_ids":["https://openalex.org/I150729083"],"apc_list":null,"apc_paid":null,"fwci":0.7226,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.8340805,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"405","last_page":"410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11236","display_name":"Control Systems and Identification","score":0.17560000717639923,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11236","display_name":"Control Systems and Identification","score":0.17560000717639923,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7995163202285767},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.6841719150543213},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6824418306350708},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.6806999444961548},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.6693738698959351},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5243435502052307},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5020537376403809},{"id":"https://openalex.org/keywords/execution-time","display_name":"Execution time","score":0.4442819654941559},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.29519975185394287}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7995163202285767},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.6841719150543213},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6824418306350708},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.6806999444961548},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.6693738698959351},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5243435502052307},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5020537376403809},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.4442819654941559},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.29519975185394287},{"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/date.2010.5457169","is_oa":false,"landing_page_url":"https://doi.org/10.1109/date.2010.5457169","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 Design, Automation &amp; Test in Europe Conference &amp; Exhibition (DATE 2010)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1598336441","https://openalex.org/W1997868137","https://openalex.org/W2007362861","https://openalex.org/W2058797440","https://openalex.org/W2059848742","https://openalex.org/W2060171832","https://openalex.org/W2101275817","https://openalex.org/W2120345843","https://openalex.org/W2125838338","https://openalex.org/W2127053227","https://openalex.org/W2136874833","https://openalex.org/W2150427812"],"related_works":["https://openalex.org/W2111241003","https://openalex.org/W4200391368","https://openalex.org/W2210979487","https://openalex.org/W2074043759","https://openalex.org/W3042736233","https://openalex.org/W2082487009","https://openalex.org/W2373535795","https://openalex.org/W2146872326","https://openalex.org/W2518118925","https://openalex.org/W3159273459"],"abstract_inverted_index":{"As":[0],"new":[1],"protein":[2,11,28,45,135],"sequences":[3],"are":[4],"discovered":[5],"on":[6,64,180],"an":[7],"everyday":[8],"basis":[9],"and":[10,23,47,49,137,147,159],"databases":[12,29],"continue":[13],"to":[14,26,30,55,85,116,166,170,174],"grow":[15],"exponentially":[16],"with":[17],"time,":[18,88],"computational":[19],"tools":[20,43],"take":[21],"more":[22,24,122],"time":[25],"search":[27,46],"discover":[31],"the":[32,40,75,82,95,100,105,110,130,160,175],"common":[33],"ancestors":[34],"of":[35,94,99,107,109],"them.":[36],"HMMER":[37,101,177],"is":[38],"among":[39],"most":[41],"used":[42],"in":[44],"comparison":[48],"multiple":[50],"efforts":[51],"have":[52],"been":[53],"made":[54],"accelerate":[56],"its":[57],"execution":[58,87,131,145],"by":[59,103],"using":[60],"dedicated":[61],"hardware":[62,144,157],"prototyped":[63],"FPGAs.":[65],"In":[66],"this":[67],"paper":[68],"we":[69,163],"introduce":[70],"a":[71,121,181],"novel":[72],"algorithm":[73,98],"called":[74],"Divergence":[76,161],"Algorithm,":[77,162],"which":[78],"not":[79,149],"only":[80,142],"enables":[81,91],"FPGA":[83],"accelerator":[84,158],"reduce":[86],"but":[89],"also":[90,119],"further":[92],"acceleration":[93],"alignment":[96,151],"generation":[97,152],"programs":[102],"reducing":[104],"number":[106],"cells":[108],"Dynamic":[111],"Programming":[112],"matrices":[113],"it":[114],"has":[115],"calculate.":[117],"We":[118],"propose":[120],"accurate":[123],"performance":[124],"measurement":[125],"strategy":[126],"that":[127],"considers":[128],"all":[129],"times":[132,146],"while":[133,139],"doing":[134],"searches":[136],"alignments,":[138],"other":[140],"works":[141],"consider":[143],"do":[148],"include":[150],"times.":[153],"Using":[154],"our":[155],"proposed":[156],"were":[164],"able":[165],"achieve":[167],"gains":[168],"up":[169],"182\u00d7":[171],"when":[172],"compared":[173],"unaccelerated":[176],"software":[178],"running":[179],"general":[182],"purpose":[183],"CPU.":[184]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-01-28T23:14:49.684275","created_date":"2025-10-10T00:00:00"}
