{"id":"https://openalex.org/W2023226967","doi":"https://doi.org/10.1145/1046192.1046222","title":"Hyper customized processors for bio-sequence database scanning on FPGAs","display_name":"Hyper customized processors for bio-sequence database scanning on FPGAs","publication_year":2005,"publication_date":"2005-02-20","ids":{"openalex":"https://openalex.org/W2023226967","doi":"https://doi.org/10.1145/1046192.1046222","mag":"2023226967"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1145/1046192.1046222","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"proceedings-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/A5111680033","display_name":"Tim 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":"Tim Oliver","raw_affiliation_strings":["Nanyang Technological University (Singapore)"],"affiliations":[{"raw_affiliation_string":"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":"Bertil Schmidt","raw_affiliation_strings":["Nanyang Technological University (Singapore)"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University (Singapore)","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","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":"Douglas Maskell","raw_affiliation_strings":["Nanyang Technological University (Singapore)"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University (Singapore)","institution_ids":["https://openalex.org/I172675005"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.863,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":103,"citation_normalized_percentile":{"value":0.981908,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"229","last_page":"237"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994,"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":0.9994,"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":0.9976,"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":0.9949,"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/speedup","display_name":"Speedup","score":0.81572235},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.62429595},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.52190685},{"id":"https://openalex.org/keywords/performance-improvement","display_name":"Performance Improvement","score":0.42529404}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.81572235},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.78400993},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.75052917},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.6739893},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.62429595},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5574395},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.52190685},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.51352984},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.42562854},{"id":"https://openalex.org/C2778915421","wikidata":"https://www.wikidata.org/wiki/Q3643177","display_name":"Performance improvement","level":2,"score":0.42529404},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.26663804},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26212794},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.18284076},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.119415164},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07733515},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"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/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1145/1046192.1046222","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":21,"referenced_works":["https://openalex.org/W1502621331","https://openalex.org/W1507071772","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/W2137503802","https://openalex.org/W2140598222","https://openalex.org/W2142574874","https://openalex.org/W2148853951","https://openalex.org/W2156264615","https://openalex.org/W2163680465","https://openalex.org/W2173952877","https://openalex.org/W2306133747","https://openalex.org/W4285719527","https://openalex.org/W86339357"],"related_works":["https://openalex.org/W4384937382","https://openalex.org/W2811338992","https://openalex.org/W2783918938","https://openalex.org/W2753093005","https://openalex.org/W2171474230","https://openalex.org/W2143599190","https://openalex.org/W2127279938","https://openalex.org/W2045575721","https://openalex.org/W1980160788","https://openalex.org/W1482324242"],"abstract_inverted_index":{"Protein":[0],"sequences":[1,13],"with":[2],"unknown":[3],"functionality":[4],"are":[5,38,87],"often":[6],"compared":[7,139],"to":[8,14,40,46,58,67,105,112,140,155],"a":[9,55,93,123,141],"set":[10],"of":[11,76,92,116,125],"known":[12],"detect":[15],"functional":[16],"similarities.":[17],"Efficient":[18,74],"dynamic-programming":[19],"algorithms":[20],"exist":[21],"for":[22,128,134],"solving":[23],"this":[24,51],"problem,":[25],"however":[26],"current":[27],"solutions":[28],"still":[29],"require":[30],"significant":[31],"scan":[32,35],"times.":[33],"These":[34],"time":[36],"requirements":[37],"likely":[39],"become":[41],"even":[42],"more":[43],"severe":[44],"due":[45],"exponential":[47],"database":[48,60],"growth.":[49],"In":[50],"paper":[52],"we":[53],"present":[54],"new":[56],"approach":[57],"bio-sequence":[59],"scanning":[61],"using":[62,80],"re-configurable":[63],"FPGA-based":[64],"hardware":[65],"platforms":[66],"gain":[68],"high":[69],"performance":[70],"at":[71,103,150],"low":[72],"cost.":[73],"mappings":[75],"the":[77,90,109,158],"Smith-Waterman":[78],"algorithm":[79],"fine-grained":[81],"parallel":[82],"processing":[83],"elements":[84],"(PEs)":[85],"that":[86],"tailored":[88],"towards":[89],"parameters":[91],"query":[94],"have":[95],"been":[96],"designed.":[97],"We":[98,146],"use":[99,115],"customization":[100],"opportunities":[101],"available":[102,117],"run-time":[104,151],"dynamically":[106],"hyper":[107],"customize":[108],"systolic":[110],"array":[111],"make":[113],"better":[114],"resource.":[118],"Our":[119],"FPGA":[120],"implementation":[121],"achieves":[122],"speedup":[124],"approximately":[126],"170":[127],"linear":[129],"gap":[130,136],"penalties":[131,137],"and":[132],"125":[133],"affine":[135],"as":[138],"standard":[142],"desktop":[143],"computing":[144],"platform.":[145],"show":[147],"how":[148],"hyper-customization":[149],"can":[152],"be":[153],"used":[154],"further":[156],"improve":[157],"performance.":[159]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2023226967","counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":7}],"updated_date":"2024-12-09T21:08:58.568511","created_date":"2016-06-24"}