{"id":"https://openalex.org/W4247044463","doi":"https://doi.org/10.1109/tetc.2021.3093840","title":"ALPHA: A Novel Algorithm-Hardware Co-Design for Accelerating DNA Seed Location Filtering","display_name":"ALPHA: A Novel Algorithm-Hardware Co-Design for Accelerating DNA Seed Location Filtering","publication_year":2021,"publication_date":"2021-07-02","ids":{"openalex":"https://openalex.org/W4247044463","doi":"https://doi.org/10.1109/tetc.2021.3093840"},"language":"en","primary_location":{"id":"doi:10.1109/tetc.2021.3093840","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tetc.2021.3093840","pdf_url":null,"source":{"id":"https://openalex.org/S2496326734","display_name":"IEEE Transactions on Emerging Topics in Computing","issn_l":"2168-6750","issn":["2168-6750","2376-4562"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Emerging Topics in Computing","raw_type":"journal-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/A5070038996","display_name":"Fazal Hameed","orcid":"https://orcid.org/0000-0002-2763-8755"},"institutions":[{"id":"https://openalex.org/I197827452","display_name":"Institute of Space Technology","ror":"https://ror.org/01tmmzv45","country_code":"PK","type":"education","lineage":["https://openalex.org/I197827452"]},{"id":"https://openalex.org/I4405266956","display_name":"Center for Advancing Electronics Dresden","ror":"https://ror.org/00g3vrr12","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]},{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE","PK"],"is_corresponding":false,"raw_author_name":"Fazal Hameed","raw_affiliation_strings":["Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany","Institute of Space Technologies (IST), Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]},{"raw_affiliation_string":"Institute of Space Technologies (IST), Islamabad, Pakistan","institution_ids":["https://openalex.org/I197827452"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090070224","display_name":"Asif Ali Khan","orcid":"https://orcid.org/0000-0002-5130-9855"},"institutions":[{"id":"https://openalex.org/I4405266956","display_name":"Center for Advancing Electronics Dresden","ror":"https://ror.org/00g3vrr12","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]},{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Asif Ali Khan","raw_affiliation_strings":["Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5130-9855","affiliations":[{"raw_affiliation_string":"Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030115692","display_name":"Jer\u00f3nimo Castrill\u00f3n","orcid":"https://orcid.org/0000-0002-5007-445X"},"institutions":[{"id":"https://openalex.org/I4405266956","display_name":"Center for Advancing Electronics Dresden","ror":"https://ror.org/00g3vrr12","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]},{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jeronimo Castrillon","raw_affiliation_strings":["Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5007-445X","affiliations":[{"raw_affiliation_string":"Chair for Compiler Construction and the Center for Advancing Electronics Dresden (cfaed), Technische Universit&#x00E4;t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I4405266956","https://openalex.org/I78650965"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4441,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.59620307,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"10","issue":"3","first_page":"1464","last_page":"1475"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9988999962806702,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9905999898910522,"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/computer-science","display_name":"Computer science","score":0.8160861134529114},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7521374225616455},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5893051028251648},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5833403468132019},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.5647392272949219},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.4939790368080139},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.44021403789520264},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.41763630509376526},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.32729780673980713},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.22579333186149597}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8160861134529114},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7521374225616455},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5893051028251648},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5833403468132019},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.5647392272949219},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.4939790368080139},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.44021403789520264},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.41763630509376526},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.32729780673980713},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.22579333186149597},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tetc.2021.3093840","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tetc.2021.3093840","pdf_url":null,"source":{"id":"https://openalex.org/S2496326734","display_name":"IEEE Transactions on Emerging Topics in Computing","issn_l":"2168-6750","issn":["2168-6750","2376-4562"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Emerging Topics in Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.9100000262260437,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W794840634","https://openalex.org/W1828154403","https://openalex.org/W1919257374","https://openalex.org/W1994576782","https://openalex.org/W2074231493","https://openalex.org/W2082346787","https://openalex.org/W2082375193","https://openalex.org/W2087064593","https://openalex.org/W2096791516","https://openalex.org/W2105102111","https://openalex.org/W2112893969","https://openalex.org/W2116412478","https://openalex.org/W2119305840","https://openalex.org/W2124715997","https://openalex.org/W2139747296","https://openalex.org/W2140673900","https://openalex.org/W2153527981","https://openalex.org/W2168303240","https://openalex.org/W2194172909","https://openalex.org/W2204664557","https://openalex.org/W2211504288","https://openalex.org/W2471077310","https://openalex.org/W2560228154","https://openalex.org/W2581980648","https://openalex.org/W2606571143","https://openalex.org/W2761132374","https://openalex.org/W2766890412","https://openalex.org/W2789843538","https://openalex.org/W2790091177","https://openalex.org/W2883847355","https://openalex.org/W2902947058","https://openalex.org/W2912837441","https://openalex.org/W2964849163","https://openalex.org/W2971433408","https://openalex.org/W2971559821","https://openalex.org/W2979449748","https://openalex.org/W2981619930","https://openalex.org/W3013588319","https://openalex.org/W3046494740","https://openalex.org/W3101704407","https://openalex.org/W3103269557","https://openalex.org/W3105003914","https://openalex.org/W3111187134","https://openalex.org/W6645529534","https://openalex.org/W6732831629"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2135248929","https://openalex.org/W2092690310","https://openalex.org/W330130819","https://openalex.org/W2798440551","https://openalex.org/W2357461155","https://openalex.org/W2384129116","https://openalex.org/W3190662310","https://openalex.org/W2354251581","https://openalex.org/W2047588290"],"abstract_inverted_index":{"Sequence":[0],"alignment":[1,28,126],"is":[2,61,130,135],"a":[3,17,24,55,116,195],"fundamental":[4],"operation":[5,140,240],"in":[6,74,80,115,222,235,257],"genomic":[7],"analysis":[8,72],"where":[9],"DNA":[10,20],"fragments":[11],"called":[12],"reads":[13,106],"are":[14,41,218],"mapped":[15],"to":[16,243],"long":[18],"reference":[19],"sequence.":[21],"There":[22],"exist":[23],"number":[25,248],"of":[26,48,58,70,90,124,153,184,249],"(in)exact":[27],"algorithms":[29,73,79],"with":[30],"varying":[31],"sensitivity":[32],"for":[33,104,200,206],"both":[34],"local":[35],"and":[36,68,76,107,190,197,204,264,269],"global":[37],"alignments,":[38],"however,":[39],"they":[40],"all":[42],"computationally":[43],"expensive.":[44],"With":[45],"the":[46,66,71,77,88,91,101,122,125,138,151,154,163,177,181,188,201,207,223,233,236,244,247,261],"advent":[47],"high-throughput":[49],"sequencing":[50],"(HTS)":[51],"technologies":[52],"that":[53,99,112,137,216,231],"generate":[54],"mammoth":[56],"amount":[57,183],"data,":[59],"there":[60,217],"increased":[62],"pressure":[63],"on":[64,86,176],"improving":[65,87],"performance":[67,89,123,196,263],"capacity":[69],"general":[75],"mapping":[78,102,110],"particular.":[81],"While":[82],"many":[83],"works":[84],"focus":[85],"aligner":[92],"themselves,":[93],"recently":[94,164],"it":[95,134,147],"has":[96],"been":[97],"demonstrated":[98],"restricting":[100],"space":[103],"input":[105,212],"filtering":[108,139,224,239],"out":[109],"positions":[111],"will":[113],"result":[114],"poor":[117],"match":[118],"can":[119,141,148],"significantly":[120,144],"improve":[121],"operation.":[127,225],"However,":[128,180],"this":[129,158],"only":[131],"true":[132],"if":[133],"guaranteed":[136],"be":[142],"performed":[143],"faster.":[145],"Otherwise,":[146],"easily":[149],"outweigh":[150],"benefits":[152],"aligner.":[155],"To":[156],"expedite":[157],"pre-alignment":[159],"filtering,":[160],"among":[161],"others,":[162],"proposed":[165],"GRIM-Filter":[166],"uses":[167],"highly-parallel":[168],"processing-in-memory":[169],"operations":[170],"benefiting":[171],"from":[172],"light-weight":[173],"computational":[174],"units":[175],"logic-in-memory":[178,191],"layer.":[179],"significant":[182],"data":[185],"transferring":[186],"between":[187],"memory":[189,202,250,258],"layers":[192],"quickly":[193],"becomes":[194],"energy":[198,265],"bottleneck":[199],"subsystem":[203],"ultimately":[205],"overall":[208,262],"system.":[209],"By":[210],"analyzing":[211],"genomes,":[213],"we":[214],"found":[215],"unexpected":[219],"data-reuse":[220,234],"opportunities":[221],"We":[226],"propose":[227],"an":[228],"algorithm-hardware":[229],"co-design":[230],"exploits":[232],"seed":[237],"location":[238],"and,":[241],"compared":[242],"GRIM-Filter,":[245],"cuts":[246],"accesses":[251,259],"by":[252,267],"22-54":[253],"percent.":[254],"This":[255],"reduction":[256],"improves":[260],"consumption":[266],"19-44":[268],"21-49":[270],"percent,":[271],"respectively.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
