{"id":"https://openalex.org/W4388038182","doi":"https://doi.org/10.1587/transinf.2022edp7230","title":"A Multi-FPGA Implementation of FM-Index Based Genomic Pattern Search","display_name":"A Multi-FPGA Implementation of FM-Index Based Genomic Pattern Search","publication_year":2023,"publication_date":"2023-10-31","ids":{"openalex":"https://openalex.org/W4388038182","doi":"https://doi.org/10.1587/transinf.2022edp7230"},"language":"en","primary_location":{"id":"doi:10.1587/transinf.2022edp7230","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1587/transinf.2022edp7230","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E106.D/11/E106.D_2022EDP7230/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.jstage.jst.go.jp/article/transinf/E106.D/11/E106.D_2022EDP7230/_pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062472600","display_name":"Ullah M. M. Imdad","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ullah IMDAD","raw_affiliation_strings":["Department of Information & Computer Science, Keio University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information & Computer Science, Keio University","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002677279","display_name":"Akram Ben Ahmed","orcid":"https://orcid.org/0000-0002-1253-8620"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akram BEN AHMED","raw_affiliation_strings":["National Institute of Advanced Industrial Science and Technology (AIST)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology (AIST)","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080549879","display_name":"Kazuei Hironaka","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuei HIRONAKA","raw_affiliation_strings":["Department of Information & Computer Science, Keio University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information & Computer Science, Keio University","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062174973","display_name":"Kensuke Iizuka","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kensuke IIZUKA","raw_affiliation_strings":["Department of Information & Computer Science, Keio University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information & Computer Science, Keio University","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113742339","display_name":"Hideharu Amano","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hideharu AMANO","raw_affiliation_strings":["Department of Information & Computer Science, Keio University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information & Computer Science, Keio University","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13907977,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"E106.D","issue":"11","first_page":"1783","last_page":"1795"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9939000010490417,"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":0.9939000010490417,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9921000003814697,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9851999878883362,"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":0.8661745190620422},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.793421745300293},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7680286765098572},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6420941352844238},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5598475337028503},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5127207040786743},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.41409942507743835},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.36165115237236023},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10159456729888916}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8661745190620422},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.793421745300293},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7680286765098572},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6420941352844238},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5598475337028503},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5127207040786743},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.41409942507743835},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.36165115237236023},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10159456729888916},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1587/transinf.2022edp7230","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1587/transinf.2022edp7230","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E106.D/11/E106.D_2022EDP7230/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1587/transinf.2022edp7230","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1587/transinf.2022edp7230","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E106.D/11/E106.D_2022EDP7230/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4399999976158142,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1259820951","display_name":null,"funder_award_id":"JPMJCR19K1","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388038182.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1566539040","https://openalex.org/W1992519395","https://openalex.org/W1999309919","https://openalex.org/W2011175593","https://openalex.org/W2015831381","https://openalex.org/W2025347051","https://openalex.org/W2029195137","https://openalex.org/W2037113830","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2095905530","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2107824361","https://openalex.org/W2142619120","https://openalex.org/W2146496959","https://openalex.org/W2158322625","https://openalex.org/W2158714788","https://openalex.org/W2161488606","https://openalex.org/W2170551349","https://openalex.org/W2319458729","https://openalex.org/W2330100020","https://openalex.org/W2475840367","https://openalex.org/W2599597882","https://openalex.org/W2608579164","https://openalex.org/W2883929540","https://openalex.org/W2904445802","https://openalex.org/W2913329744","https://openalex.org/W2942646047","https://openalex.org/W2945306514","https://openalex.org/W2990314330","https://openalex.org/W3013901498","https://openalex.org/W3109100377","https://openalex.org/W3131073178","https://openalex.org/W3194143084","https://openalex.org/W3214824440","https://openalex.org/W3217251616","https://openalex.org/W4200412744","https://openalex.org/W4200421000","https://openalex.org/W4210801615","https://openalex.org/W4254502766","https://openalex.org/W4256629673","https://openalex.org/W4280575288","https://openalex.org/W4281901797"],"related_works":["https://openalex.org/W2111241003","https://openalex.org/W1970433854","https://openalex.org/W4200391368","https://openalex.org/W2210979487","https://openalex.org/W2023867642","https://openalex.org/W2074043759","https://openalex.org/W1905852083","https://openalex.org/W575709247","https://openalex.org/W2389214306","https://openalex.org/W3042736233"],"abstract_inverted_index":{"FPGA":[0,6,22,42],"clusters":[1],"that":[2,210],"consist":[3],"of":[4,51,87],"multiple":[5,52],"boards":[7,72,224,228],"have":[8],"been":[9],"gaining":[10],"interest":[11],"in":[12,169,182,203],"recent":[13],"times.":[14],"Massively":[15],"parallel":[16,89,170,176,183],"processing":[17],"with":[18,24,33,44,65,221],"a":[19,40,135,194,211,219],"stand-alone":[20],"heterogeneous":[21,41],"cluster":[23,43],"SoC-":[25],"style":[26],"FPGAs":[27,30,58],"and":[28,46,59,111,184,218,225],"mid-scale":[29],"is":[31,123,150,206],"promising":[32],"cost-performance":[34],"benefit.":[35],"Here,":[36],"we":[37,92],"propose":[38],"such":[39],"FiC":[45,49,76,216,227],"M-KUBOS":[47,71,212,223],"cluster.":[48],"consists":[50],"boards,":[53,217],"mounting":[54],"middle":[55],"scale":[56],"Xilinx's":[57],"DRAMs,":[60],"which":[61,178],"are":[62,73,131,144],"tightly":[63],"coupled":[64],"high-speed":[66],"serial":[67],"links.":[68],"In":[69],"addition,":[70],"connected":[74],"to":[75,134,157],"for":[77,153,171],"ensuring":[78],"high":[79],"IO":[80],"data":[81,195,204],"transfer":[82],"bandwidth.":[83],"As":[84],"an":[85],"example":[86],"massively":[88,175],"processing,":[90],"here":[91],"implement":[93,193],"genomic":[94,117],"pattern":[95,141,148],"search.":[96],"Next-generation":[97],"sequencing":[98],"(NGS)":[99],"technology":[100],"has":[101],"revolutionized":[102],"biological":[103],"system":[104,220],"related":[105],"research":[106],"by":[107],"its":[108],"high-speed,":[109],"scalable":[110],"massive":[112],"throughput.":[113],"To":[114],"analyze":[115],"the":[116,158,174,186,234],"data,":[118,173,180],"short":[119,126],"read":[120],"mapping":[121,160],"technique":[122],"used":[124],"where":[125,198],"Deoxyribonucleic":[127],"acid":[128],"(DNA)":[129],"sequences":[130],"mapped":[132],"relative":[133],"known":[136,162],"reference":[137],"sequence.":[138],"Although":[139],"several":[140],"matching":[142,165],"techniques":[143],"available,":[145],"FM-index":[146],"based":[147,236],"search":[149],"perfectly":[151],"suitable":[152],"this":[154],"task":[155],"due":[156],"fastest":[159],"from":[161],"indices.":[163],"Since":[164],"can":[166,188],"be":[167,189],"done":[168],"different":[172],"computing":[177],"distributes":[179],"executes":[181],"gathers":[185],"results":[187],"applied.":[190],"We":[191,208],"also":[192],"compression":[196],"method":[197],"about":[199],"10":[200],"times":[201,231],"reduction":[202],"size":[205],"achieved.":[207],"found":[209],"board":[213],"matches":[214],"four":[215],"six":[222],"24":[226],"achieved":[229],"30":[230],"faster":[232],"than":[233],"software":[235],"implementation.":[237]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}