{"id":"https://openalex.org/W2962735533","doi":"https://doi.org/10.1093/bioinformatics/btx596","title":"FMtree: a fast locating algorithm of FM-indexes for genomic data","display_name":"FMtree: a fast locating algorithm of FM-indexes for genomic data","publication_year":2017,"publication_date":"2017-09-16","ids":{"openalex":"https://openalex.org/W2962735533","doi":"https://doi.org/10.1093/bioinformatics/btx596","mag":"2962735533","pmid":"https://pubmed.ncbi.nlm.nih.gov/28968761"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx596","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/3/416/25117149/btx596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/3/416/25117149/btx596.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044987443","display_name":"Haoyu Cheng","orcid":"https://orcid.org/0000-0002-9209-5793"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyu Cheng","raw_affiliation_strings":["Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China","Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100744728","display_name":"Ming Wu","orcid":"https://orcid.org/0000-0002-4972-3686"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming Wu","raw_affiliation_strings":["Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105471307","display_name":"Yun Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yun Xu","raw_affiliation_strings":["Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China","Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"Key Laboratory on High Performance Computing, Anhui Province, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"School of Computer Science, University of Science and Technology of China, Heifei, Anhui, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5105471307"],"corresponding_institution_ids":["https://openalex.org/I126520041","https://openalex.org/I170215575"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3988,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.74114447,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"34","issue":"3","first_page":"416","last_page":"424"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9072999954223633,"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":0.9072999954223633,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.009800000116229057,"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":0.006399999838322401,"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":0.8162707090377808},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.6858841180801392},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5470479726791382},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5219635367393494},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.5045615434646606},{"id":"https://openalex.org/keywords/traverse","display_name":"Traverse","score":0.47446566820144653},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44615206122398376},{"id":"https://openalex.org/keywords/locality","display_name":"Locality","score":0.4346993863582611},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.42902472615242004},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11036163568496704}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8162707090377808},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.6858841180801392},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5470479726791382},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5219635367393494},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.5045615434646606},{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.47446566820144653},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44615206122398376},{"id":"https://openalex.org/C2779808786","wikidata":"https://www.wikidata.org/wiki/Q6664603","display_name":"Locality","level":2,"score":0.4346993863582611},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.42902472615242004},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11036163568496704},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx596","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/3/416/25117149/btx596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28968761","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28968761","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx596","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/3/416/25117149/btx596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2962735533.pdf","grobid_xml":"https://content.openalex.org/works/W2962735533.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W794840634","https://openalex.org/W1493802692","https://openalex.org/W1534435001","https://openalex.org/W1548907175","https://openalex.org/W1603565140","https://openalex.org/W1967156765","https://openalex.org/W2000586119","https://openalex.org/W2015853171","https://openalex.org/W2025648894","https://openalex.org/W2041445031","https://openalex.org/W2046038806","https://openalex.org/W2068589160","https://openalex.org/W2088386938","https://openalex.org/W2093516854","https://openalex.org/W2097341408","https://openalex.org/W2105708056","https://openalex.org/W2109262879","https://openalex.org/W2110327674","https://openalex.org/W2115501618","https://openalex.org/W2119305840","https://openalex.org/W2158874082","https://openalex.org/W2167943254","https://openalex.org/W2168602018","https://openalex.org/W2170551349","https://openalex.org/W2170899819","https://openalex.org/W2191136822","https://openalex.org/W2593228764","https://openalex.org/W2952380754","https://openalex.org/W6629522497","https://openalex.org/W6639872743","https://openalex.org/W6764480365"],"related_works":["https://openalex.org/W96331545","https://openalex.org/W1548907175","https://openalex.org/W2583658747","https://openalex.org/W1517600056","https://openalex.org/W2160738675","https://openalex.org/W2036633468","https://openalex.org/W2405149725","https://openalex.org/W2396668937","https://openalex.org/W2041306856","https://openalex.org/W2003608043"],"abstract_inverted_index":{"Motivation:":[0],"As":[1,139],"a":[2,13,49,81,100,119,122,135,140],"fundamental":[3],"task":[4],"in":[5,61,80],"bioinformatics,":[6],"searching":[7,31,117],"for":[8,88,118],"massive":[9],"short":[10],"patterns":[11,79,90],"over":[12,121],"long":[14],"text":[15],"has":[16],"been":[17],"accelerated":[18],"by":[19,152],"various":[20],"compressed":[21,53],"full-text":[22,54],"indexes.":[23],"These":[24],"indexes":[25],"are":[26,84,210],"able":[27],"to":[28,33,105],"provide":[29],"similar":[30],"functionalities":[32],"classical":[34],"indexes,":[35,55],"e.g.":[36],"suffix":[37,40],"trees":[38],"and":[39,171,192,196],"arrays,":[41],"while":[42],"requiring":[43],"less":[44],"space.":[45],"For":[46],"genomic":[47],"data,":[48],"well-known":[50],"family":[51],"of":[52,66,78,111,130,145,168,185],"called":[56],"FM-indexes,":[57],"presents":[58,172],"unmatched":[59],"performance":[60],"practice.":[62],"One":[63],"major":[64],"drawback":[65],"FM-indexes":[67],"is":[68,181,199],"that":[69,179],"their":[70],"locating":[71,102,132,160],"operations,":[72],"which":[73],"report":[74],"all":[75,108],"occurrence":[76,109,143],"positions":[77,110,144],"given":[82,123],"text,":[83,124],"not":[85],"efficient,":[86],"especially":[87],"the":[89,127,131,154,189],"with":[91,158],"many":[92],"occurrences.":[93],"Results:":[94],"In":[95],"this":[96,146],"paper,":[97],"we":[98],"introduce":[99],"novel":[101],"algorithm,":[103],"FMtree,":[104],"fast":[106],"retrieve":[107],"any":[112],"pattern":[113,120,147],"via":[114],"FM-indexes.":[115],"When":[116],"FMtree":[125,180,198],"organizes":[126],"search":[128],"space":[129],"operation":[133],"into":[134],"conceptual":[136],"multiway":[137,155],"tree.":[138,156],"result,":[141],"multiple":[142],"can":[148],"be":[149],"retrieved":[150],"simultaneously":[151],"traversing":[153],"Compared":[157],"existing":[159],"algorithms,":[161,191],"our":[162],"tree-based":[163],"algorithm":[164],"reduces":[165],"large":[166],"numbers":[167],"redundant":[169],"operations":[170],"better":[173],"data":[174,209],"locality.":[175],"Experimental":[176],"results":[177],"show":[178],"usually":[182],"one":[183],"order":[184],"magnitude":[186],"faster":[187],"than":[188],"state-of-the-art":[190],"still":[193],"memory-efficient.":[194],"Availability":[195],"implementation:":[197],"freely":[200],"available":[201,211],"at":[202,212],"https://github.com/chhylp123/FMtree.":[203],"Contact:":[204],"xuyun@ustc.edu.cn.":[205],"Supplementary":[206,208],"information:":[207],"Bioinformatics":[213],"online.":[214]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
