{"id":"https://openalex.org/W2154932989","doi":"https://doi.org/10.1109/iscas.2005.1465706","title":"A Reconfigurable Architecture for Scanning Biosequence Databases","display_name":"A Reconfigurable Architecture for Scanning Biosequence Databases","publication_year":2005,"publication_date":"2005-07-27","ids":{"openalex":"https://openalex.org/W2154932989","doi":"https://doi.org/10.1109/iscas.2005.1465706","mag":"2154932989"},"language":"en","primary_location":{"id":"doi:10.1109/iscas.2005.1465706","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iscas.2005.1465706","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2005 IEEE International Symposium on Circuits and Systems","raw_type":"proceedings-article"},"type":"conference-paper","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/A5111920345","display_name":"T. Oliver","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"T. Oliver","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"B. Schmidt","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059218594","display_name":"Douglas L. Maskell","orcid":"https://orcid.org/0000-0002-6588-4762"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"D.L. Maskell","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042105714","display_name":"A. P. Vinod","orcid":"https://orcid.org/0000-0001-9408-1275"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"A.P. Vinod","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2438","issue":null,"first_page":"4799","last_page":"4802"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9987000226974487,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9886000156402588,"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":0.7918484210968018},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7817853689193726},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.5947190523147583},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5904603004455566},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5272623300552368},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.45455774664878845},{"id":"https://openalex.org/keywords/reconfigurable-computing","display_name":"Reconfigurable computing","score":0.43821483850479126},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.39066267013549805},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.32905203104019165},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12892010807991028}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7918484210968018},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7817853689193726},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.5947190523147583},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5904603004455566},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5272623300552368},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.45455774664878845},{"id":"https://openalex.org/C142962650","wikidata":"https://www.wikidata.org/wiki/Q240838","display_name":"Reconfigurable computing","level":3,"score":0.43821483850479126},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.39066267013549805},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.32905203104019165},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12892010807991028},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/iscas.2005.1465706","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iscas.2005.1465706","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2005 IEEE International Symposium on Circuits and Systems","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-106826","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-106826","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"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":"Conference paper"},{"id":"pmh:oai:repository.ust.hk:1783.1-106826","is_oa":false,"landing_page_url":"http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=0271-4310&rft.volume=&rft.issue=&rft.date=2005&rft.spage=4799&rft.aulast=Oliver&rft.aufirst=&rft.atitle=A+reconfigurable+architecture+for+scanning+biosequence+databases&rft.title=Proceedings+-+IEEE+International+Symposium+on+Circuits+and+Systems","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference paper"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W86339357","https://openalex.org/W1566539040","https://openalex.org/W1594783879","https://openalex.org/W1935349158","https://openalex.org/W1966118102","https://openalex.org/W1973959475","https://openalex.org/W2055043387","https://openalex.org/W2072763119","https://openalex.org/W2087064593","https://openalex.org/W2112547256","https://openalex.org/W2126613433","https://openalex.org/W2140598222","https://openalex.org/W2142574874","https://openalex.org/W2148853951","https://openalex.org/W2163680465","https://openalex.org/W2168135110","https://openalex.org/W2173952877","https://openalex.org/W4236236547","https://openalex.org/W6634012511","https://openalex.org/W6635629768","https://openalex.org/W6668594571","https://openalex.org/W6681053179","https://openalex.org/W6685446562"],"related_works":["https://openalex.org/W1612076744","https://openalex.org/W2126857316","https://openalex.org/W2152074211","https://openalex.org/W2129019972","https://openalex.org/W3164085601","https://openalex.org/W1522032972","https://openalex.org/W2113308450","https://openalex.org/W1967938402","https://openalex.org/W2386041993","https://openalex.org/W2139962137"],"abstract_inverted_index":{"Unknown":[0],"protein":[1],"sequences":[2,11],"are":[3,41,111],"often":[4],"compared":[5],"to":[6,15,43,66,76,85],"a":[7,73,117,129],"set":[8],"of":[9,49,55,63,100,116],"known":[10],"(a":[12],"database":[13,78],"scan)":[14],"detect":[16],"functional":[17],"similarities.":[18],"Even":[19],"though":[20],"efficient":[21,95],"dynamic":[22],"programming":[23],"algorithms":[24],"exist":[25],"for":[26],"this":[27,69,98],"problem,":[28],"the":[29,50,114],"required":[30],"scanning":[31,79],"time":[32,39],"is":[33,62],"still":[34],"very":[35],"high.":[36],"The":[37],"scan":[38],"requirements":[40],"likely":[42],"become":[44],"even":[45],"more":[46],"severe":[47],"because":[48],"rapid":[51],"growth":[52],"in":[53,68,121],"size":[54],"these":[56],"databases.":[57],"Thus,":[58],"finding":[59],"fast":[60],"solutions":[61],"high":[64,87],"importance":[65],"research":[67],"area.":[70],"We":[71],"present":[72],"new":[74],"approach":[75],"biosequence":[77],"using":[80],"reconfigurable":[81],"FPGA-based":[82],"hardware":[83],"platforms":[84],"gain":[86],"performance":[88],"at":[89],"low":[90],"cost.":[91],"To":[92],"derive":[93],"an":[94,122],"mapping":[96],"onto":[97],"type":[99],"architecture,":[101],"we":[102],"have":[103],"designed":[104],"fine-grained":[105],"parallel":[106],"processing":[107],"elements":[108],"(PEs)":[109],"that":[110],"tailored":[112],"towards":[113],"parameters":[115],"query.":[118],"This":[119],"results":[120],"implementation":[123],"with":[124],"significant":[125],"runtime":[126],"savings":[127],"on":[128],"standard":[130],"FPGA.":[131]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
