{"id":"https://openalex.org/W2132634714","doi":"https://doi.org/10.1109/asap.2013.6567581","title":"BioBlaze: Multi-core SIMD ASIP for DNA sequence alignment","display_name":"BioBlaze: Multi-core SIMD ASIP for DNA sequence alignment","publication_year":2013,"publication_date":"2013-06-01","ids":{"openalex":"https://openalex.org/W2132634714","doi":"https://doi.org/10.1109/asap.2013.6567581","mag":"2132634714"},"language":"en","primary_location":{"id":"doi:10.1109/asap.2013.6567581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/asap.2013.6567581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE 24th International Conference on Application-Specific Systems, Architectures and Processors","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/3429994","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058701648","display_name":"Nuno Neves","orcid":"https://orcid.org/0000-0003-0628-2259"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Nuno Neves","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021116534","display_name":"Nuno Sebasti\u00e3o","orcid":"https://orcid.org/0000-0001-9537-0554"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno Sebastiao","raw_affiliation_strings":["IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029850501","display_name":"Andr\u00e9 Patr\u00edcio","orcid":"https://orcid.org/0000-0002-4841-4371"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Andre Patricio","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089103785","display_name":"David Martins de Matos","orcid":"https://orcid.org/0000-0001-8631-2870"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"David Matos","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075054918","display_name":"Pedro Tom\u00e1s","orcid":"https://orcid.org/0000-0001-8083-4432"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Tomas","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002334825","display_name":"Paulo Flores","orcid":"https://orcid.org/0000-0003-2970-3589"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Paulo Flores","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015710714","display_name":"Nuno Roma","orcid":"https://orcid.org/0000-0003-2491-4977"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno Roma","raw_affiliation_strings":["INESC-ID, IST, Lisboa, Portugal","IST/INESC-ID, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, IST, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"IST/INESC-ID, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5058701648"],"corresponding_institution_ids":["https://openalex.org/I121345201"],"apc_list":null,"apc_paid":null,"fwci":1.1697,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.78487398,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"241","last_page":"244"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976000189781189,"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":0.9976000189781189,"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":0.9970999956130981,"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/T12029","display_name":"DNA and Biological Computing","score":0.9868000149726868,"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/computer-science","display_name":"Computer science","score":0.8623419404029846},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.8079527020454407},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.7955940365791321},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7625831365585327},{"id":"https://openalex.org/keywords/instruction-set","display_name":"Instruction set","score":0.6806641221046448},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6293399930000305},{"id":"https://openalex.org/keywords/application-specific-instruction-set-processor","display_name":"Application-specific instruction-set processor","score":0.5392289161682129},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.49298712611198425},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4765216112136841},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.38380685448646545},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.24244412779808044},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08730104565620422}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8623419404029846},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.8079527020454407},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.7955940365791321},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7625831365585327},{"id":"https://openalex.org/C202491316","wikidata":"https://www.wikidata.org/wiki/Q272683","display_name":"Instruction set","level":2,"score":0.6806641221046448},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6293399930000305},{"id":"https://openalex.org/C201736964","wikidata":"https://www.wikidata.org/wiki/Q621583","display_name":"Application-specific instruction-set processor","level":3,"score":0.5392289161682129},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.49298712611198425},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4765216112136841},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.38380685448646545},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.24244412779808044},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08730104565620422}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/asap.2013.6567581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/asap.2013.6567581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE 24th International Conference on Application-Specific Systems, Architectures and Processors","raw_type":"proceedings-article"},{"id":"pmh:oai:zenodo.org:3429994","is_oa":true,"landing_page_url":"https://zenodo.org/record/3429994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencePaper"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:3429994","is_oa":true,"landing_page_url":"https://zenodo.org/record/3429994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencePaper"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1991217739","https://openalex.org/W2015442306","https://openalex.org/W2068448872","https://openalex.org/W2087064593","https://openalex.org/W2095540795","https://openalex.org/W2146379626","https://openalex.org/W2162852139","https://openalex.org/W4256075606"],"related_works":["https://openalex.org/W2099629705","https://openalex.org/W1992352827","https://openalex.org/W2047885859","https://openalex.org/W2036206036","https://openalex.org/W3012895752","https://openalex.org/W2045177269","https://openalex.org/W2994245508","https://openalex.org/W2189543321","https://openalex.org/W4242172182","https://openalex.org/W2116582200"],"abstract_inverted_index":{"A":[0,119],"new":[1],"Application-Specific":[2],"Instruction-set":[3],"Processor":[4],"(ASIP)":[5],"architecture":[6,17],"for":[7],"biological":[8],"sequences":[9,73],"alignment":[10],"is":[11,31,63],"proposed":[12,103,135,153],"in":[13,74,132,168],"this":[14],"manuscript.":[15],"This":[16],"achieves":[18,155],"high":[19],"processing":[20],"throughputs":[21],"by":[22,33,65,166],"exploiting":[23],"both":[24,133],"fine":[25],"and":[26,53,58,107,121,137,183],"coarse-grained":[27],"parallelism.":[28],"The":[29,102,174],"former":[30],"achieved":[32,64,146],"extending":[34],"the":[35,86,96,127,134,145,152,162,169,177,190],"Instruction":[36],"Set":[37],"Architecture":[38],"(ISA)":[39],"of":[40,95,126,176,192],"a":[41,75,88,110,115,122,156],"synthesizable":[42],"processor":[43],"to":[44,69,185],"include":[45],"multiple":[46,67,72],"specialized":[47],"SIMD":[48,124],"instructions":[49],"that":[50,151],"implement":[51],"vector-vector":[52],"vector-scalar":[54],"arithmetic,":[55],"logic,":[56],"load/store":[57],"control":[59],"operations.":[60],"Coarse-grained":[61],"parallelism":[62],"using":[66],"cores":[68],"cooperatively":[70],"align":[71],"shared":[76],"memory":[77],"architecture,":[78],"comprising":[79],"proper":[80],"hardware-specific":[81],"synchronization":[82],"mechanisms.":[83],"To":[84],"ease":[85],"programming,":[87],"compilation":[89],"framework":[90],"based":[91],"on":[92,109],"an":[93,138],"adaptation":[94],"GCC":[97],"back-end":[98],"was":[99,105,149,180],"also":[100,181],"implemented.":[101],"system":[104,179],"prototyped":[106],"evaluated":[108,182],"Xilinx":[111],"Virtex-7":[112],"FPGA,":[113],"achieving":[114],"200MHz":[116],"working":[117],"frequency.":[118],"sequential":[120],"state-of-theart":[123],"implementations":[125],"Smith-Waterman":[128],"algorithm":[129],"were":[130],"programmed":[131],"ASIP":[136],"Intel":[139,170],"Core":[140,171],"i7":[141,172],"processor.":[142,173],"When":[143],"comparing":[144],"speedups,":[147],"it":[148],"observed":[150],"ISA":[154],"40x":[157],"speedup,":[158],"which":[159],"contrasts":[160],"with":[161,189],"11x":[163],"speedup":[164],"provided":[165],"SSE2":[167],"scalability":[175],"multi-core":[178],"proved":[184],"scale":[186],"almost":[187],"linearly":[188],"number":[191],"cores.":[193]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
