{"id":"https://openalex.org/W4406271590","doi":"https://doi.org/10.1109/bibm62325.2024.10822058","title":"ParaSAT: a scalable parallel framework for sequence alignment","display_name":"ParaSAT: a scalable parallel framework for sequence alignment","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271590","doi":"https://doi.org/10.1109/bibm62325.2024.10822058"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822058","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822058","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5089996987","display_name":"Wenjuan Liu","orcid":"https://orcid.org/0000-0003-0973-111X"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wenjuan Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032768716","display_name":"J.X. Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianbang Xu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061621381","display_name":"Liangrui Pan","orcid":"https://orcid.org/0000-0003-0565-4217"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liangrui Pan","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105471967","display_name":"Tommaso Cai","orcid":"https://orcid.org/0000-0002-7234-3526"},"institutions":[{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tie Cai","raw_affiliation_strings":["Hunan University,Shenzhen Institute of Information Technology (SZIIT),Shenzhen,China"],"affiliations":[{"raw_affiliation_string":"Hunan University,Shenzhen Institute of Information Technology (SZIIT),Shenzhen,China","institution_ids":["https://openalex.org/I158809036"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108008219","display_name":"Shaoliang Peng","orcid":"https://orcid.org/0000-0002-4647-2615"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoliang Peng","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5089996987"],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19130621,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1054","last_page":"1059"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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":0.9666000008583069,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9553999900817871,"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":0.7752357721328735},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7280235886573792},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6520867347717285},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5112361907958984},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09627637267112732},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08739456534385681}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7752357721328735},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7280235886573792},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6520867347717285},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5112361907958984},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09627637267112732},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08739456534385681},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822058","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822058","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1519266993","https://openalex.org/W2004148449","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2106882534","https://openalex.org/W2141978199","https://openalex.org/W2158714788","https://openalex.org/W2160378127","https://openalex.org/W2161471331","https://openalex.org/W2194172909","https://openalex.org/W2241590652","https://openalex.org/W2789843538","https://openalex.org/W2919864984","https://openalex.org/W3146294934","https://openalex.org/W3197178642","https://openalex.org/W6703514187"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4401278057"],"abstract_inverted_index":{"Sequence":[0],"alignment":[1,37,41,57,119,151],"is":[2,49],"a":[3,43,76,123],"fundamental":[4],"step":[5],"in":[6,63],"genomic":[7,18,157],"data":[8,19,26,158],"analysis.":[9],"Third-generation":[10],"sequencing":[11,25],"technology":[12],"facilitates":[13],"the":[14,21,64,88,95,98,114,147],"acquisition":[15],"of":[16,24,90,97,149],"high-quality":[17],"but":[20],"explosive":[22],"growth":[23],"poses":[27],"huge":[28],"challenges":[29],"to":[30,54,61,68,87,104],"current":[31],"sequence":[32,36,56,118,150],"alignment.":[33],"To":[34,93],"reduce":[35],"time":[38],"and":[39,58,121,142,152],"enhance":[40],"performance,":[42],"parallelization":[44],"framework":[45,116,138],"based":[46],"on":[47,107,126],"Minimap2":[48],"proposed,":[50],"called":[51],"ParaSAT,":[52],"aiming":[53],"expedite":[55],"offer":[59],"insights":[60],"researchers":[62],"field.":[65],"In":[66],"order":[67],"achieve":[69],"load":[70],"balancing":[71],"among":[72],"multi-nodes,":[73],"We":[74,100],"design":[75],"task":[77],"pool":[78],"scheduling":[79],"strategy":[80],"which":[81],"can":[82],"dynamically":[83],"distribute":[84],"tasks":[85],"according":[86],"status":[89],"compute":[91],"nodes.":[92],"evaluate":[94],"performance":[96],"framework,":[99],"choose":[101],"6":[102],"dataset":[103],"conduct":[105],"experiments":[106],"TH-1":[108],"supercomputer.":[109],"The":[110,137],"outcomes":[111],"confirm":[112],"that":[113],"parallel":[115,132],"ensures":[117],"accuracy,":[120],"demonstrates":[122],"notable":[124],"speedup":[125],"large":[127],"datasets,":[128],"approaching":[129],"linearity,":[130],"with":[131],"efficiency":[133,148],"consistently":[134],"above":[135],"80%.":[136],"also":[139],"exhibits":[140],"strong":[141],"weak":[143],"scalability,":[144],"effectively":[145],"enhancing":[146],"offering":[153],"guidance":[154],"for":[155],"high-performance":[156],"processing.":[159]},"counts_by_year":[],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
