{"id":"https://openalex.org/W2108502925","doi":"https://doi.org/10.1109/bibe.2008.4696722","title":"High performance FPGA-based core for BLAST sequence alignment with the two-hit method","display_name":"High performance FPGA-based core for BLAST sequence alignment with the two-hit method","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2108502925","doi":"https://doi.org/10.1109/bibe.2008.4696722","mag":"2108502925"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","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/A5018240924","display_name":"Server Kasap","orcid":"https://orcid.org/0000-0001-6408-1338"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Server Kasap","raw_affiliation_strings":["University of Edinburgh, Edinburgh, UK","University of Edinburgh, Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh, Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104706884","display_name":"Khaled Benkrid","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Khaled Benkrid","raw_affiliation_strings":["University of Edinburgh, Edinburgh, UK","University of Edinburgh, Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh, Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100414245","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0002-4966-3476"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["University of Edinburgh, Edinburgh, UK","University of Edinburgh, Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh, Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I98677209"],"apc_list":null,"apc_paid":null,"fwci":0.5616,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68091451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"48","issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9986000061035156,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998199999332428,"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/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.8556740283966064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8060723543167114},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.8048919439315796},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5902197360992432},{"id":"https://openalex.org/keywords/parameterized-complexity","display_name":"Parameterized complexity","score":0.545246958732605},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5241641998291016},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.51505446434021},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4993879795074463},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.45135343074798584},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4446902871131897},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.4315427839756012},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.37487876415252686},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3534737527370453},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.3533955216407776},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.25707489252090454},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17947381734848022},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1498149037361145}],"concepts":[{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.8556740283966064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8060723543167114},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.8048919439315796},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5902197360992432},{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.545246958732605},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5241641998291016},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.51505446434021},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4993879795074463},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.45135343074798584},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4446902871131897},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.4315427839756012},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.37487876415252686},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3534737527370453},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.3533955216407776},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.25707489252090454},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17947381734848022},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1498149037361145},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2008.4696722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1536639965","https://openalex.org/W2009570821","https://openalex.org/W2015292449","https://openalex.org/W2043198910","https://openalex.org/W2054388411","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2112547256","https://openalex.org/W2142574874","https://openalex.org/W2148853951","https://openalex.org/W2156264615","https://openalex.org/W2158714788","https://openalex.org/W2254458779","https://openalex.org/W2995746888","https://openalex.org/W3149451194","https://openalex.org/W4236236547","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W2391207559","https://openalex.org/W2717174904","https://openalex.org/W2352639277","https://openalex.org/W2548545698","https://openalex.org/W2092936829","https://openalex.org/W2025467172"],"abstract_inverted_index":{"This":[0,90],"paper":[1,36],"presents":[2],"the":[3,18,38,58,83,88,130,139,154],"design":[4],"and":[5,34,65,67,96,165],"implementation":[6,42],"of":[7,43,50,57,73,77,82,108],"a":[8,25,93],"high":[9,94],"performance":[10,95],"FPGA-based":[11],"core":[12,52,118,131],"for":[13],"BLAST":[14,21],"sequence":[15,31,59],"alignment":[16,32],"with":[17,22,87],"two-hit":[19,23],"method.":[20],"is":[24,37,53,71,119],"very":[26],"widely":[27],"used":[28],"heuristic":[29],"biological":[30],"algorithm,":[33],"this":[35],"first":[39],"reported":[40],"FPGA":[41,98,163],"it,":[44],"to":[45,142,161],"our":[46,51,117],"knowledge.":[47],"The":[48],"architecture":[49],"parameterized":[54],"in":[55,85,92,134],"terms":[56],"lengths,":[60],"match":[61],"scores,":[62],"gap":[63],"penalties,":[64],"cut-off":[66],"threshold":[68],"values.":[69],"It":[70],"composed":[72],"various":[74],"blocks":[75],"each":[76],"which":[78,100,143],"performs":[79],"one":[80,106],"step":[81],"algorithm":[84],"parallel":[86],"others.":[89],"results":[91],"efficient":[97],"implementation,":[99],"outperforms":[101],"equivalent":[102,124],"software":[103,125],"implementations":[104,114],"by":[105],"order":[107],"magnitude":[109],"or":[110,148],"more.":[111],"Real":[112],"hardware":[113],"show":[115],"that":[116],"52":[120],"times":[121],"faster":[122],"than":[123],"implementations,":[126],"on":[127],"average.":[128],"Furthermore,":[129],"was":[132],"captured":[133],"an":[135],"FPGA-platform-independent":[136],"language,":[137,141],"namely":[138],"Handel-C":[140],"no":[144],"specific":[145],"resource":[146],"inference":[147],"placement":[149],"constraints":[150],"were":[151],"applied.":[152],"Hence,":[153],"same":[155],"code":[156],"can":[157],"be":[158],"easily":[159],"ported":[160],"different":[162],"families":[164],"architectures.":[166]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
