{"id":"https://openalex.org/W2761496944","doi":"https://doi.org/10.23919/fpl.2017.8056838","title":"Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts","display_name":"Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts","publication_year":2017,"publication_date":"2017-09-01","ids":{"openalex":"https://openalex.org/W2761496944","doi":"https://doi.org/10.23919/fpl.2017.8056838","mag":"2761496944"},"language":"en","primary_location":{"id":"doi:10.23919/fpl.2017.8056838","is_oa":false,"landing_page_url":"https://doi.org/10.23919/fpl.2017.8056838","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 27th International Conference on Field Programmable Logic and Applications (FPL)","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/A5056411319","display_name":"Ho-Cheung Ng","orcid":"https://orcid.org/0000-0002-5171-1318"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ho-Cheung Ng","raw_affiliation_strings":["Department of Computing, Imperial College, London, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, Imperial College, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101818400","display_name":"Shuanglong Liu","orcid":"https://orcid.org/0000-0002-1513-1981"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shuanglong Liu","raw_affiliation_strings":["Department of Computing, Imperial College, London, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, Imperial College, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057940557","display_name":"Wayne Luk","orcid":"https://orcid.org/0000-0002-6750-927X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wayne Luk","raw_affiliation_strings":["Department of Computing, Imperial College, London, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, Imperial College, London, UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5056411319"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":null,"apc_paid":null,"fwci":1.2309,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.79274472,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9968000054359436,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8558387756347656},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.8302916884422302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7984410524368286},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.5560626983642578},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5291717052459717},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.5067904591560364},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5026168823242188},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48898446559906006},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47864043712615967},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46765273809432983},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.45492711663246155},{"id":"https://openalex.org/keywords/genetic-programming","display_name":"Genetic programming","score":0.4430704116821289},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.42769643664360046},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.4261713922023773},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3721942901611328},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23989444971084595},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20412710309028625},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17203688621520996},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.13645267486572266}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8558387756347656},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.8302916884422302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7984410524368286},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5560626983642578},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5291717052459717},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.5067904591560364},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5026168823242188},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48898446559906006},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47864043712615967},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46765273809432983},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.45492711663246155},{"id":"https://openalex.org/C110332635","wikidata":"https://www.wikidata.org/wiki/Q629498","display_name":"Genetic programming","level":2,"score":0.4430704116821289},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.42769643664360046},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.4261713922023773},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3721942901611328},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23989444971084595},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20412710309028625},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17203688621520996},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.13645267486572266},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.23919/fpl.2017.8056838","is_oa":false,"landing_page_url":"https://doi.org/10.23919/fpl.2017.8056838","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 27th International Conference on Field Programmable Logic and Applications (FPL)","raw_type":"proceedings-article"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/56330","is_oa":false,"landing_page_url":"http://hdl.handle.net/10044/1/56330","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2017 27th International Conference on Field Programmable Logic and Applications (FPL)","raw_type":"Conference Paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G600182179","display_name":null,"funder_award_id":"EP/L00058X/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7493804148","display_name":null,"funder_award_id":"EP/N031768/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G774180880","display_name":null,"funder_award_id":"EP/P010040/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":103,"referenced_works":["https://openalex.org/W28246465","https://openalex.org/W163711237","https://openalex.org/W1566539040","https://openalex.org/W1573552135","https://openalex.org/W1589754454","https://openalex.org/W1594783879","https://openalex.org/W1608326296","https://openalex.org/W1864817015","https://openalex.org/W1978885894","https://openalex.org/W1979778642","https://openalex.org/W1981644820","https://openalex.org/W1985681048","https://openalex.org/W1987197389","https://openalex.org/W1988651200","https://openalex.org/W1991782483","https://openalex.org/W1992440403","https://openalex.org/W1992519395","https://openalex.org/W1995448823","https://openalex.org/W1997446138","https://openalex.org/W2006899413","https://openalex.org/W2006947318","https://openalex.org/W2009570821","https://openalex.org/W2011175593","https://openalex.org/W2013697960","https://openalex.org/W2023226967","https://openalex.org/W2026029521","https://openalex.org/W2027266885","https://openalex.org/W2030072194","https://openalex.org/W2034798008","https://openalex.org/W2036295979","https://openalex.org/W2039693716","https://openalex.org/W2039824819","https://openalex.org/W2043198910","https://openalex.org/W2052601433","https://openalex.org/W2058712496","https://openalex.org/W2060022314","https://openalex.org/W2072193858","https://openalex.org/W2074231493","https://openalex.org/W2082346787","https://openalex.org/W2086072057","https://openalex.org/W2087064593","https://openalex.org/W2095680943","https://openalex.org/W2095905530","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2103644816","https://openalex.org/W2106318735","https://openalex.org/W2106882534","https://openalex.org/W2108502925","https://openalex.org/W2109243933","https://openalex.org/W2111305378","https://openalex.org/W2112113834","https://openalex.org/W2112131781","https://openalex.org/W2115069592","https://openalex.org/W2115303170","https://openalex.org/W2115872073","https://openalex.org/W2119501327","https://openalex.org/W2120594828","https://openalex.org/W2123629203","https://openalex.org/W2124985265","https://openalex.org/W2126626169","https://openalex.org/W2127380362","https://openalex.org/W2131417499","https://openalex.org/W2139548488","https://openalex.org/W2140350225","https://openalex.org/W2142574874","https://openalex.org/W2142599417","https://openalex.org/W2143180875","https://openalex.org/W2144316495","https://openalex.org/W2144597359","https://openalex.org/W2144745211","https://openalex.org/W2146496959","https://openalex.org/W2153923325","https://openalex.org/W2154826966","https://openalex.org/W2156976066","https://openalex.org/W2158714788","https://openalex.org/W2159224090","https://openalex.org/W2161488606","https://openalex.org/W2163764537","https://openalex.org/W2163997137","https://openalex.org/W2167408328","https://openalex.org/W2168077168","https://openalex.org/W2218392081","https://openalex.org/W2302950296","https://openalex.org/W2330100020","https://openalex.org/W2404756046","https://openalex.org/W2515042543","https://openalex.org/W2537255992","https://openalex.org/W2587851098","https://openalex.org/W3140730966","https://openalex.org/W3150677990","https://openalex.org/W4241026011","https://openalex.org/W4245668478","https://openalex.org/W4246147816","https://openalex.org/W4285719527","https://openalex.org/W4394666350","https://openalex.org/W6601191515","https://openalex.org/W6606710089","https://openalex.org/W6654031322","https://openalex.org/W6680795761","https://openalex.org/W6683504902","https://openalex.org/W6684251070","https://openalex.org/W6698112302"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2891987081","https://openalex.org/W2532502681"],"abstract_inverted_index":{"Genetic":[0],"sequence":[1,25],"alignment":[2],"has":[3,57],"always":[4],"been":[5,59],"a":[6,28,70,79],"computational":[7],"challenge":[8],"in":[9,31],"bioinformatics.":[10],"Depending":[11],"on":[12,83,107],"the":[13,24,50,74],"problem":[14],"size,":[15],"software-based":[16],"aligners":[17],"can":[18,37],"take":[19],"multiple":[20],"CPU-days":[21],"to":[22,68,98,104],"process":[23],"data,":[26],"creating":[27],"bottleneck":[29],"point":[30],"bioinformatic":[32],"analysis":[33],"flow.":[34],"Reconfigurable":[35],"accelerator":[36],"achieve":[38],"high":[39],"performance":[40],"for":[41,101,111],"such":[42],"computation":[43],"by":[44,62,77],"providing":[45],"massive":[46],"parallelism,":[47],"but":[48],"at":[49],"expense":[51],"of":[52,73],"programming":[53],"flexibility":[54],"and":[55,86,103],"thus":[56],"not":[58],"commensurately":[60],"used":[61],"practitioners.":[63],"Therefore,":[64],"this":[65],"paper":[66],"aims":[67],"provide":[69,105],"thorough":[71],"survey":[72],"proposed":[75],"accelerators":[76],"giving":[78],"qualitative":[80],"categorization":[81],"based":[82],"their":[84],"algorithms":[85],"speedup.":[87],"A":[88],"comprehensive":[89],"comparison":[90],"between":[91],"work":[92],"is":[93],"also":[94],"presented":[95],"so":[96],"as":[97],"guide":[99],"selection":[100],"biologist,":[102],"insight":[106],"future":[108],"research":[109],"direction":[110],"FPGA":[112],"scientists.":[113]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
