{"id":"https://openalex.org/W2411730464","doi":"https://doi.org/10.1093/bioinformatics/btw345","title":"KCMBT: a <i>k</i>-mer Counter based on Multiple Burst Trees","display_name":"KCMBT: a <i>k</i>-mer Counter based on Multiple Burst Trees","publication_year":2016,"publication_date":"2016-06-09","ids":{"openalex":"https://openalex.org/W2411730464","doi":"https://doi.org/10.1093/bioinformatics/btw345","mag":"2411730464","pmid":"https://pubmed.ncbi.nlm.nih.gov/27283950"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw345","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2783/24406878/btw345.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/32/18/2783/24406878/btw345.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100970396","display_name":"Abdullah-Al Mamun","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abdullah-Al Mamun","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086885083","display_name":"Soumitra Pal","orcid":"https://orcid.org/0000-0003-4840-3944"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soumitra Pal","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034177039","display_name":"Sanguthevar Rajasekaran","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sanguthevar Rajasekaran","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5034177039"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2849,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.91930139,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"18","first_page":"2783","last_page":"2790"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.6154000163078308,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.6154000163078308,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.28279998898506165,"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/T11269","display_name":"Algorithms and Data Compression","score":0.05700000002980232,"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/substring","display_name":"Substring","score":0.9279350638389587},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.9093688130378723},{"id":"https://openalex.org/keywords/trie","display_name":"Trie","score":0.7177411913871765},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6965557336807251},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6434640884399414},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5419012904167175},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.47997355461120605},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4529912769794464},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.41579023003578186},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.3741723597049713},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32233762741088867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1719372272491455},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1566801369190216},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11520883440971375}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.9279350638389587},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.9093688130378723},{"id":"https://openalex.org/C190290938","wikidata":"https://www.wikidata.org/wiki/Q387015","display_name":"Trie","level":3,"score":0.7177411913871765},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6965557336807251},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6434640884399414},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5419012904167175},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.47997355461120605},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4529912769794464},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.41579023003578186},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3741723597049713},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32233762741088867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1719372272491455},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1566801369190216},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11520883440971375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw345","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2783/24406878/btw345.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:27283950","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27283950","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},{"id":"pmh:oai:europepmc.org:5027264","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5939891","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/18/2783","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/18/2783","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw345","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2783/24406878/btw345.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":[{"id":"https://openalex.org/G1198520646","display_name":"BIGDATA: F: DKA: DKM: Novel Out-of-core and Parallel Algorithms for Processing Biological Big Data","funder_award_id":"1447711","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1429836112","display_name":null,"funder_award_id":"R01 LM010101","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G5520316217","display_name":null,"funder_award_id":"NIH-R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8470911175","display_name":"Efficient Algorithms for Motif Search","funder_award_id":"5r01lm010101-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2411730464.pdf","grobid_xml":"https://content.openalex.org/works/W2411730464.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1992950355","https://openalex.org/W2014099509","https://openalex.org/W2027667941","https://openalex.org/W2037444377","https://openalex.org/W2057253402","https://openalex.org/W2060233189","https://openalex.org/W2076747312","https://openalex.org/W2096128575","https://openalex.org/W2096634299","https://openalex.org/W2097066660","https://openalex.org/W2111307596","https://openalex.org/W2123845384","https://openalex.org/W2125266506","https://openalex.org/W2133956160","https://openalex.org/W2136651963","https://openalex.org/W2160265768","https://openalex.org/W2160770624","https://openalex.org/W2160969485","https://openalex.org/W2163584430","https://openalex.org/W2171003081","https://openalex.org/W6665489941"],"related_works":["https://openalex.org/W2950956043","https://openalex.org/W2278452282","https://openalex.org/W2411730464","https://openalex.org/W2461862277","https://openalex.org/W2121927033","https://openalex.org/W2148315173","https://openalex.org/W597455093","https://openalex.org/W1929174210","https://openalex.org/W3034799230","https://openalex.org/W3168674043"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1,17],"massive":[2],"number":[3],"of":[4,9,23],"bioinformatics":[5],"applications":[6,43],"require":[7],"counting":[8,82],"k-length":[10,25],"substrings":[11],"in":[12,27,62,69],"genetically":[13],"important":[14],"long":[15],"strings.":[16],"k-mer":[18,46,81,89],"counter":[19,47],"generates":[20],"the":[21,113,148],"frequencies":[22],"each":[24],"substring":[26],"genome":[28,120],"sequences.":[29],"Genome":[30],"assembly,":[31],"repeat":[32],"detection,":[33],"multiple":[34,153],"sequence":[35],"alignment,":[36],"error":[37],"detection":[38],"and":[39,54],"many":[40],"other":[41],"related":[42],"use":[44],"a":[45,49,75],"as":[48],"building":[50],"block.":[51],"Very":[52],"fast":[53],"efficient":[55],"algorithms":[56,149],"are":[57,171],"necessary":[58],"to":[59,66],"count":[60],"k-mers":[61],"large":[63],"data":[64,144,170],"sets":[65,145],"be":[67],"useful":[68],"such":[70],"applications.":[71],"RESULTS:":[72],"We":[73,84],"propose":[74],"novel":[76],"trie-based":[77],"algorithm":[78,88,116,126],"for":[79,118],"this":[80],"problem.":[83],"compare":[85],"our":[86,125],"devised":[87],"Counter":[90],"based":[91],"on":[92,141,162],"Multiple":[93],"Burst":[94],"Trees":[95],"(KCMBT)":[96],"with":[97],"available":[98,161,172],"all":[99],"well-known":[100],"algorithms.":[101],"Our":[102],"experimental":[103],"results":[104],"show":[105],"that":[106],"KCMBT":[107,135,158],"is":[108,127,136,159],"around":[109,128],"30%":[110],"faster":[111,131,138],"than":[112,132,139],"previous":[114],"best-performing":[115],"KMC2":[117,140],"human":[119],"dataset.":[121],"As":[122],"another":[123],"example,":[124],"six":[129],"times":[130],"Jellyfish2.":[133],"Overall,":[134],"20-30%":[137],"five":[142],"benchmark":[143],"when":[146],"both":[147],"were":[150],"run":[151],"using":[152],"threads.":[154],"AVAILABILITY":[155],"AND":[156],"IMPLEMENTATION:":[157],"freely":[160],"GitHub:":[163],"(https://github.com/abdullah009/kcmbt_mt).":[164],"CONTACT:":[165],"rajasek@engr.uconn.edu":[166],"SUPPLEMENTARY":[167],"INFORMATION:":[168],"Supplementary":[169],"at":[173],"Bioinformatics":[174],"online.":[175]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2016-06-24T00:00:00"}
