{"id":"https://openalex.org/W2537255992","doi":"https://doi.org/10.1109/hpec.2012.6408669","title":"Multithreaded FPGA acceleration of DNA sequence mapping","display_name":"Multithreaded FPGA acceleration of DNA sequence mapping","publication_year":2012,"publication_date":"2012-09-01","ids":{"openalex":"https://openalex.org/W2537255992","doi":"https://doi.org/10.1109/hpec.2012.6408669","mag":"2537255992"},"language":"en","primary_location":{"id":"doi:10.1109/hpec.2012.6408669","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpec.2012.6408669","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Conference on High Performance Extreme Computing","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/A5019120974","display_name":"Edward B. Fernandez","orcid":null},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Edward B. Fernandez","raw_affiliation_strings":["University of California Riverside Riverside, USA"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033921328","display_name":"Walid Najjar","orcid":"https://orcid.org/0000-0001-6761-6801"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walid A. Najjar","raw_affiliation_strings":["University of California Riverside Riverside, USA"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042005042","display_name":"Stefano Lonardi","orcid":"https://orcid.org/0000-0002-2696-7274"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefano Lonardi","raw_affiliation_strings":["University of California Riverside Riverside, USA"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012012492","display_name":"Jason Villarreal","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jason Villarreal","raw_affiliation_strings":["Jacquard Computing Inc. Riverside, USA"],"affiliations":[{"raw_affiliation_string":"Jacquard Computing Inc. Riverside, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019120974"],"corresponding_institution_ids":["https://openalex.org/I103635307"],"apc_list":null,"apc_paid":null,"fwci":2.653,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.91182395,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9993000030517578,"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":0.9757000207901001,"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":0.8561275601387024},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6897476315498352},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6074478030204773},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.5404118299484253},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5139426589012146},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5096347332000732},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.4499196410179138},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4158724546432495},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2670847177505493}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8561275601387024},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6897476315498352},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6074478030204773},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.5404118299484253},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5139426589012146},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5096347332000732},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.4499196410179138},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4158724546432495},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2670847177505493},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/hpec.2012.6408669","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpec.2012.6408669","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Conference on High Performance Extreme Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307791","display_name":"Cisco Systems","ror":"https://ror.org/03yt1ez60"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"},{"id":"https://openalex.org/F4320338294","display_name":"Air Force Research Laboratory","ror":"https://ror.org/02e2egq70"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1991782483","https://openalex.org/W1992519395","https://openalex.org/W2013697960","https://openalex.org/W2024710847","https://openalex.org/W2055058950","https://openalex.org/W2081040934","https://openalex.org/W2103441770","https://openalex.org/W2115303170","https://openalex.org/W2116495135","https://openalex.org/W2120594828","https://openalex.org/W2124985265","https://openalex.org/W2126626169","https://openalex.org/W2127380362","https://openalex.org/W2142574874","https://openalex.org/W2143180875","https://openalex.org/W2144316495","https://openalex.org/W2144745211","https://openalex.org/W2146496959","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2622728018","https://openalex.org/W4244381167","https://openalex.org/W6677476193"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W1590307681","https://openalex.org/W2536018345","https://openalex.org/W4312814274","https://openalex.org/W4285370786","https://openalex.org/W2518118925","https://openalex.org/W3159273459","https://openalex.org/W3152699334"],"abstract_inverted_index":{"In":[0,114],"bioinformatics,":[1],"short":[2,15,57,135],"read":[3,58,69,136],"alignment":[4,137],"is":[5],"a":[6,20,28,46,52,125,131,232],"computationally":[7],"intensive":[8],"operation":[9],"that":[10,48,128,227],"involves":[11],"matching":[12],"millions":[13,36],"of":[14,26,35,37,39,41,51,67,79,155,182,186,206,241],"strings":[16],"(called":[17],"reads)":[18],"against":[19,45,208,250],"reference":[21,85],"genome.":[22,86],"At":[23],"the":[24,65,77,106,161,176,183,191,194,204,211,239],"time":[25],"writing,":[27],"representative":[29],"run":[30],"requires":[31],"to":[32,62,75,103,159,164,190,217,231,246],"match":[33],"tens":[34],"reads":[38,83],"length":[40],"about":[42],"100":[43],"symbols":[44],"genome":[47],"can":[49,97],"consists":[50,154],"few":[53,233],"billion":[54],"characters.":[55],"Existing":[56],"aligners":[59],"are":[60],"expected":[61],"report":[63],"all":[64],"occurrences":[66],"each":[68],"as":[70,72,91,130],"well":[71],"allow":[73],"users":[74],"control":[76],"number":[78],"allowed":[80],"mismatches":[81],"between":[82,198],"and":[84,153,172,193,200],"Popular":[87],"software":[88],"implementations":[89],"such":[90],"Bowtie":[92,209],"[8]":[93],"or":[94,101],"BWA":[95],"[10]":[96],"take":[98,228],"many":[99,146],"hours":[100,230],"days":[102],"execute,":[104],"making":[105],"problem":[107],"an":[108,167],"ideal":[109],"candidate":[110],"for":[111,134],"hardware":[112,126,148,199],"acceleration.":[113],"this":[115],"paper,":[116],"we":[117,214],"describe":[118],"FHAST":[119,174,207,245],"(FPGA":[120],"Hardware":[121],"Accelerated":[122],"Sequencing-matching":[123],"Tool),":[124],"accelerator":[127],"acts":[129],"drop-in":[132],"replacement":[133],"software.":[138,201],"Our":[139],"architecture":[140],"masks":[141],"memory":[142,151,187,196],"latency":[143],"by":[144],"executing":[145],"concurrent":[147],"threads":[149],"accessing":[150],"simultaneously":[152],"multiple":[156,248,251],"parallel":[157],"engines":[158],"exploit":[160],"parallelism":[162],"available":[163,189],"us":[165],"on":[166,175,210],"FPGA.":[168],"We":[169,235],"have":[170],"implemented":[171],"tested":[173],"Convey":[177,212],"HC-1":[178,213],"[9],":[179],"taking":[180],"advantage":[181],"large":[184],"amount":[185],"bandwidth":[188],"system":[192],"shared":[195],"image":[197],"By":[202],"comparing":[203],"performance":[205],"observed":[215],"up":[216],"~70X":[218],"improvement":[219],"in":[220,253],"total":[221],"end-to-end":[222],"execution":[223],"time,":[224],"reducing":[225],"runs":[226],"several":[229],"minutes.":[234],"also":[236],"favorably":[237],"compare":[238],"rate":[240],"growth":[242],"when":[243],"expanding":[244],"utilize":[247],"FPGAs":[249],"CPUs":[252],"Bowtie.":[254]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}