{"id":"https://openalex.org/W1971208552","doi":"https://doi.org/10.1145/1854776.1854792","title":"An annotated <i>k</i> -deep prefix tree for (1- <i>k</i> )-mer based sequence comparisons","display_name":"An annotated <i>k</i> -deep prefix tree for (1- <i>k</i> )-mer based sequence comparisons","publication_year":2010,"publication_date":"2010-08-02","ids":{"openalex":"https://openalex.org/W1971208552","doi":"https://doi.org/10.1145/1854776.1854792","mag":"1971208552"},"language":"en","primary_location":{"id":"doi:10.1145/1854776.1854792","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5084824924","display_name":"Adrienne Breland","orcid":null},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrienne Breland","raw_affiliation_strings":["University of Nevada, Reno, NV"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno, NV","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037111265","display_name":"Karen Schlauch","orcid":"https://orcid.org/0000-0001-6916-8571"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen Schlauch","raw_affiliation_strings":["University of Nevada, Reno, NV"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno, NV","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043342974","display_name":"Monica Nicolescu","orcid":"https://orcid.org/0009-0009-8748-7918"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monica Nicolescu","raw_affiliation_strings":["University of Nevada, Reno, NV"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno, NV","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101893887","display_name":"J. S. Harris","orcid":"https://orcid.org/0000-0002-0857-6931"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frederick C. Harris","raw_affiliation_strings":["University of Nevada, Reno, NV"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno, NV","institution_ids":["https://openalex.org/I134113660"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I134113660"],"apc_list":null,"apc_paid":null,"fwci":0.9236,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.74084919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":null,"first_page":"79","last_page":"85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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":0.9972000122070312,"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/prefix","display_name":"Prefix","score":0.824196457862854},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.7895777225494385},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.7082158923149109},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6665035486221313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.592943549156189},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.5612627267837524},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.4988715648651123},{"id":"https://openalex.org/keywords/k-ary-tree","display_name":"K-ary tree","score":0.4722957909107208},{"id":"https://openalex.org/keywords/trie","display_name":"Trie","score":0.4601048231124878},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39489805698394775},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.39057299494743347},{"id":"https://openalex.org/keywords/tree-structure","display_name":"Tree structure","score":0.3643820881843567},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.311872273683548},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2757185995578766},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2517053782939911},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.2169579565525055},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.15633907914161682},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13567396998405457},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10636827349662781}],"concepts":[{"id":"https://openalex.org/C141603448","wikidata":"https://www.wikidata.org/wiki/Q134830","display_name":"Prefix","level":2,"score":0.824196457862854},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.7895777225494385},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.7082158923149109},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6665035486221313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.592943549156189},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.5612627267837524},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.4988715648651123},{"id":"https://openalex.org/C100560664","wikidata":"https://www.wikidata.org/wiki/Q3608019","display_name":"K-ary tree","level":4,"score":0.4722957909107208},{"id":"https://openalex.org/C190290938","wikidata":"https://www.wikidata.org/wiki/Q387015","display_name":"Trie","level":3,"score":0.4601048231124878},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39489805698394775},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.39057299494743347},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.3643820881843567},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.311872273683548},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2757185995578766},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2517053782939911},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.2169579565525055},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.15633907914161682},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13567396998405457},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10636827349662781},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1854776.1854792","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W49059731","https://openalex.org/W1630386176","https://openalex.org/W1792529629","https://openalex.org/W1919001964","https://openalex.org/W2014459399","https://openalex.org/W2021809202","https://openalex.org/W2044684763","https://openalex.org/W2055043387","https://openalex.org/W2057530010","https://openalex.org/W2097706568","https://openalex.org/W2099964107","https://openalex.org/W2100301262","https://openalex.org/W2121252285","https://openalex.org/W2123135686","https://openalex.org/W2136145671","https://openalex.org/W2142619120","https://openalex.org/W2150483253","https://openalex.org/W2154478838","https://openalex.org/W4245253871","https://openalex.org/W6601992064","https://openalex.org/W6640006408"],"related_works":["https://openalex.org/W54192826","https://openalex.org/W2370594968","https://openalex.org/W4383878951","https://openalex.org/W2411730464","https://openalex.org/W2743542537","https://openalex.org/W1997112896","https://openalex.org/W2365019162","https://openalex.org/W2908418870","https://openalex.org/W2382364329","https://openalex.org/W2383075031"],"abstract_inverted_index":{"In":[0],"this":[1],"report,":[2],"we":[3],"describe":[4],"an":[5,16],"algorithm":[6,14],"for":[7,19],"a":[8,24,70,83,88,124],"k-deep":[9,125],"annotated":[10,55],"prefix":[11,126],"tree.":[12],"The":[13],"provides":[15],"alignment-free":[17],"method":[18],"comparing":[20,37],"nucleotide":[21],"sequences":[22,31,78],"in":[23,29,46,67,82,92],"computationally":[25],"efficient":[26],"manner.":[27],"Differences":[28],"genomic":[30],"are":[32,54],"measured":[33],"by":[34,98],"recording":[35],"and":[36,95,114],"counts":[38],"of":[39,41,62,69,72,110,123],"words":[40],"length":[42],"k":[43],"or":[44],"less":[45],"each":[47,64,68],"sequence":[48,103,108,131],"using":[49],"the":[50,60,121],"algorithm.":[51],"Tree":[52],"nodes":[53],"with":[56],"lists":[57],"to":[58,119],"store":[59],"number":[61],"times":[63],"word":[65],"occurs":[66],"group":[71],"sequences.":[73],"Count":[74],"differences":[75],"among":[76],"multiple":[77],"may":[79],"be":[80],"computed":[81],"single":[84],"tree":[85,89,99,127],"traversal.":[86],"Such":[87],"is":[90],"built":[91],"linear":[93],"time":[94],"spatially":[96],"bounded":[97],"depth":[100],"rather":[101],"than":[102],"length(s).":[104],"We":[105],"then":[106],"compare":[107],"groups":[109],"both":[111],"E.":[112],"coli":[113],"Influenza":[115],"A":[116],"virus":[117],"H1N1":[118],"demonstrate":[120],"utilitiy":[122],"when":[128],"used":[129],"as":[130],"comparison":[132],"tool.":[133]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}