{"id":"https://openalex.org/W4399039433","doi":"https://doi.org/10.1109/tcbb.2024.3404136","title":"An Efficient Exact Algorithm for Planted Motif Search on Large DNA Sequence Datasets","display_name":"An Efficient Exact Algorithm for Planted Motif Search on Large DNA Sequence Datasets","publication_year":2024,"publication_date":"2024-05-27","ids":{"openalex":"https://openalex.org/W4399039433","doi":"https://doi.org/10.1109/tcbb.2024.3404136","pmid":"https://pubmed.ncbi.nlm.nih.gov/38801693"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3404136","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3404136","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/A5100665870","display_name":"Qiang Yu","orcid":"https://orcid.org/0000-0002-8725-6687"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiang Yu","raw_affiliation_strings":["Hangzhou Institute of Technology, Xidian University, Hangzhou, China","School of Computer Science and Technology, Xidian University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0002-8725-6687","affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Technology, Xidian University, Hangzhou, China","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050801250","display_name":"Yana Hu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yana Hu","raw_affiliation_strings":["Xi'an Research Institute, ZTE Company, Ltd., Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi'an Research Institute, ZTE Company, Ltd., Xi'an, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077187325","display_name":"Hu Xinnan","orcid":null},"institutions":[{"id":"https://openalex.org/I2250955327","display_name":"Huawei Technologies (China)","ror":"https://ror.org/00cmhce21","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250955327"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinnan Hu","raw_affiliation_strings":["Xi'an Research Institute, Huawei Technologies Company, Ltd., Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi'an Research Institute, Huawei Technologies Company, Ltd., Xi'an, China","institution_ids":["https://openalex.org/I2250955327"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024756748","display_name":"Jingfen Lan","orcid":"https://orcid.org/0000-0002-0219-5791"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingfen Lan","raw_affiliation_strings":["School of Mathematics and Statistics, Xidian University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0002-0219-5791","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5115501048","display_name":"Yang Guo","orcid":"https://orcid.org/0009-0005-6656-5703"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Guo","raw_affiliation_strings":["Hangzhou Institute of Technology, Xidian University, Hangzhou, China"],"raw_orcid":"https://orcid.org/0009-0005-6656-5703","affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Technology, Xidian University, Hangzhou, China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5557,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.69731438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"21","issue":"5","first_page":"1542","last_page":"1551"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9927999973297119,"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":0.9927999973297119,"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/T12029","display_name":"DNA and Biological Computing","score":0.9724000096321106,"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":0.9567999839782715,"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/algorithm","display_name":"Algorithm","score":0.5905410051345825},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5258867144584656},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5252703428268433},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5052786469459534},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4999353885650635},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4540853798389435},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.44507938623428345},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.37909191846847534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28346186876296997},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24381139874458313},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0778457522392273}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5905410051345825},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5258867144584656},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5252703428268433},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5052786469459534},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4999353885650635},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4540853798389435},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.44507938623428345},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.37909191846847534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28346186876296997},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24381139874458313},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0778457522392273},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3404136","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3404136","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:38801693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38801693","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":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.5199999809265137}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1486659038","https://openalex.org/W1824139226","https://openalex.org/W1977133097","https://openalex.org/W1985716977","https://openalex.org/W1998300401","https://openalex.org/W2018297222","https://openalex.org/W2023863508","https://openalex.org/W2038093918","https://openalex.org/W2041306584","https://openalex.org/W2048088032","https://openalex.org/W2101538917","https://openalex.org/W2148014281","https://openalex.org/W2163923149","https://openalex.org/W2534001869","https://openalex.org/W2898570285","https://openalex.org/W2943591933","https://openalex.org/W3021662208","https://openalex.org/W3034009801","https://openalex.org/W3047670845","https://openalex.org/W3048429615","https://openalex.org/W3090491025","https://openalex.org/W3215280906","https://openalex.org/W4200363822","https://openalex.org/W4205149713","https://openalex.org/W4220904991","https://openalex.org/W4283703944","https://openalex.org/W4284899398","https://openalex.org/W4293456843","https://openalex.org/W4382657762","https://openalex.org/W4387816747","https://openalex.org/W4396653592","https://openalex.org/W6634719314","https://openalex.org/W6635200387","https://openalex.org/W6675171846","https://openalex.org/W6762166224","https://openalex.org/W6865895481"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2073661767","https://openalex.org/W2143211236","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2103777723","https://openalex.org/W2159636084","https://openalex.org/W2610941444","https://openalex.org/W2117168988","https://openalex.org/W2154430121"],"abstract_inverted_index":{"DNA":[0,10,22,88,100,126,206],"motif":[1,23,43],"is":[2,39,163,180],"the":[3,42,54,130,134,149,152,168,188,194],"pattern":[4,153],"shared":[5],"by":[6,147,165],"similar":[7],"fragments":[8],"in":[9,17,66],"sequences,":[11,127],"which":[12,46,103],"plays":[13],"a":[14,27],"key":[15,28],"role":[16],"regulating":[18],"gene":[19],"expression,":[20],"and":[21,183],"discovery":[24,44],"has":[25],"become":[26],"research":[29],"topic.":[30],"Exact":[31],"planted":[32],"(":[33,55,141,158,195,198],"l,":[34,56,142,159],"d":[35,57,74,143,160],")-motif":[36],"search":[37],"(PMS)":[38],"one":[40],"of":[41,62,87,92,99,125,133,172,211],"approaches,":[45],"aims":[47],"to":[48,106,178],"find":[49],"from":[50],"t":[51],"sequences":[52,70,210],"all":[53],")-motifs":[58,144],"that":[59,155,167],"are":[60,81],"motifs":[61],"l":[63],"length":[64,212],"appearing":[65],"at":[67,72],"least":[68],"qt":[69],"with":[71,145],"most":[73],"mismatches.":[75],"The":[76,90],"existing":[77,135,174],"exact":[78,108,117,136],"PMS":[79,109,118,137,176],"algorithms":[80,177],"only":[82],"suitable":[83],"for":[84,122,187],"small":[85],"datasets":[86,124,208],"sequences.":[89],"development":[91],"high-throughput":[93],"sequencing":[94],"technology":[95],"generates":[96],"vast":[97],"amount":[98],"sequence":[101,207],"data,":[102],"brings":[104],"challenges":[105],"solving":[107],"problems":[110],"efficiently.":[111],"Therefore,":[112],"we":[113],"propose":[114],"an":[115],"efficient":[116],"algorithm":[119],"called":[120],"PMmotif":[121,139,179,191],"large":[123,205],"after":[128],"analyzing":[129],"time":[131,170],"complexity":[132],"algorithms.":[138],"finds":[140],"strategy":[146],"searching":[148],"branches":[150],"on":[151,204],"tree":[154],"may":[156],"contain":[157],")-motifs.":[161],"It":[162],"verified":[164],"experiments":[166],"running":[169],"ratio":[171],"some":[173],"excellent":[175],"between":[181],"14.83":[182],"58.94.":[184],"In":[185],"addition,":[186],"first":[189],"time,":[190],"can":[192],"solve":[193],"15,5":[196],")and":[197],"17,6":[199],")":[200],"challenge":[201],"problem":[202],"instances":[203],"(3000":[209],"200)":[213],"within":[214],"24":[215],"hours.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}