{"id":"https://openalex.org/W4399881007","doi":"https://doi.org/10.1109/tcbb.2024.3417517","title":"SeedHit: A GPU Friendly Pre-Align Filtering Algorithm","display_name":"SeedHit: A GPU Friendly Pre-Align Filtering Algorithm","publication_year":2024,"publication_date":"2024-06-21","ids":{"openalex":"https://openalex.org/W4399881007","doi":"https://doi.org/10.1109/tcbb.2024.3417517","pmid":"https://pubmed.ncbi.nlm.nih.gov/38905083"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3417517","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3417517","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5062830066","display_name":"Zhen Ju","orcid":"https://orcid.org/0000-0001-7720-1570"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen Ju","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0001-7720-1570","affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119272032","display_name":"Jingjing Zhang","orcid":"https://orcid.org/0000-0002-9884-4230"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingjing Zhang","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-9884-4230","affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030177095","display_name":"Xuelei Li","orcid":"https://orcid.org/0000-0002-7935-6290"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuelei Li","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056275783","display_name":"Jintao Meng","orcid":"https://orcid.org/0000-0002-6208-4102"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jintao Meng","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-6208-4102","affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037823825","display_name":"Yanjie Wei","orcid":"https://orcid.org/0000-0002-4791-7540"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanjie Wei","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-4791-7540","affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5062830066"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"],"apc_list":null,"apc_paid":null,"fwci":0.4718,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61517347,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"21","issue":"6","first_page":"1794","last_page":"1802"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10901","display_name":"Advanced Data Compression Techniques","score":0.885699987411499,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T10901","display_name":"Advanced Data Compression Techniques","score":0.885699987411499,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T11019","display_name":"Image Enhancement Techniques","score":0.8622999787330627,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T10320","display_name":"Neural Networks and Applications","score":0.8174999952316284,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6734731793403625},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.4839087426662445},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4610428512096405},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41452154517173767},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3898720145225525},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36732035875320435}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6734731793403625},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.4839087426662445},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4610428512096405},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41452154517173767},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3898720145225525},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36732035875320435}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3417517","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3417517","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38905083","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38905083","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2810253274","display_name":null,"funder_award_id":"Y2021101","funder_id":"https://openalex.org/F4320335892","funder_display_name":"Youth Innovation Promotion Association"},{"id":"https://openalex.org/G4009424769","display_name":null,"funder_award_id":"62272449","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335892","display_name":"Youth Innovation Promotion Association","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1988925586","https://openalex.org/W2006899413","https://openalex.org/W2015915218","https://openalex.org/W2055043387","https://openalex.org/W2062296203","https://openalex.org/W2065461987","https://openalex.org/W2066852475","https://openalex.org/W2087064593","https://openalex.org/W2093931624","https://openalex.org/W2096791516","https://openalex.org/W2121716038","https://openalex.org/W2170747616","https://openalex.org/W2171777347","https://openalex.org/W2560228154","https://openalex.org/W2765491147","https://openalex.org/W2891893703","https://openalex.org/W2900776157","https://openalex.org/W2923143097","https://openalex.org/W2981619930","https://openalex.org/W3111187134","https://openalex.org/W3156514638","https://openalex.org/W3177399774","https://openalex.org/W3213765778","https://openalex.org/W4205617913","https://openalex.org/W4281812964","https://openalex.org/W4388413172","https://openalex.org/W6857213791"],"related_works":["https://openalex.org/W3213381848","https://openalex.org/W2005148983","https://openalex.org/W2017587301","https://openalex.org/W2012954338","https://openalex.org/W2096672917","https://openalex.org/W2392023973","https://openalex.org/W2939411666","https://openalex.org/W1973046741","https://openalex.org/W3189307731","https://openalex.org/W2949962288"],"abstract_inverted_index":{"The":[0,145],"amount":[1],"of":[2,21,42,51,71,147],"genetic":[3],"data":[4,24,45,104],"generated":[5],"by":[6,75],"Next":[7],"Generation":[8],"Sequencing":[9],"(NGS)":[10],"technologies":[11],"grows":[12],"faster":[13],"than":[14,55],"Moore's":[15],"law.":[16],"This":[17],"necessitates":[18],"the":[19,32,39,43,68,113,141,161,172,187,197],"development":[20],"efficient":[22],"NGS":[23,44,72],"processing":[25,70],"and":[26,105,119,168,176],"analysis":[27,34],"algorithms.":[28],"A":[29],"filter":[30],"before":[31],"computationally-costly":[33],"step":[35],"can":[36,132],"significantly":[37],"reduce":[38],"run":[40],"time":[41],"analysis.":[46],"As":[47],"GPUs":[48],"are":[49],"orders":[50],"magnitude":[52],"more":[53],"powerful":[54],"CPUs,":[56],"this":[57],"paper":[58],"proposes":[59],"a":[60,90,94,107,191],"GPU-friendly":[61,118],"pre-align":[62],"filtering":[63,165],"algorithm":[64,185],"named":[65],"SeedHit":[66,77,116,131,148,170,180],"for":[67],"fast":[69],"data.":[73],"Inspired":[74],"BLAST,":[76],"counts":[78],"seed":[79],"hits":[80],"between":[81],"two":[82,163],"sequences":[83],"to":[84,196],"determine":[85],"their":[86],"similarity.":[87],"In":[88],"SeedHit,":[89],"nucleic":[91],"acid":[92],"in":[93,99],"gene":[95],"sequence":[96,136],"is":[97,117,143],"presented":[98],"binary":[100],"format.":[101],"By":[102,178],"packaging":[103],"generating":[106],"lookup":[108],"table":[109],"that":[110],"fits":[111],"into":[112,181],"L1":[114],"cache,":[115],"high-throughput.":[120],"Using":[121],"three":[122],"16":[123],"s":[124],"rRNA":[125],"datasets":[126],"from":[127],"Greengenes":[128],"as":[129],"input":[130],"reject":[133],"84%-89%":[134],"dissimilar":[135],"pairs":[137],"on":[138,156],"average":[139],"when":[140],"similarity":[142],"0.9-0.99.":[144],"throughput":[146],"achieved":[149,190],"1":[150],"T/s":[151],"(Tera":[152],"base":[153],"per":[154],"second)":[155],"3080":[157],"Ti.":[158],"Compared":[159],"with":[160],"other":[162],"GPU-based":[164],"algorithms,":[166],"GateKeeper":[167],"SneakySnake,":[169],"has":[171],"highest":[173],"rejection":[174],"rate":[175],"throughput.":[177],"incorporating":[179],"our":[182],"in-house":[183],"clustering":[184],"nGIA,":[186],"modified":[188],"nGIA":[189],"1.6-2.1":[192],"times":[193],"speedup":[194],"compared":[195],"original":[198],"version.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-04T08:30:34.212998","created_date":"2025-10-10T00:00:00"}