{"id":"https://openalex.org/W2021809202","doi":"https://doi.org/10.1109/hicss.1994.323593","title":"Generalized suffix trees for biological sequence data: applications and implementation","display_name":"Generalized suffix trees for biological sequence data: applications and implementation","publication_year":1994,"publication_date":"1994-01-01","ids":{"openalex":"https://openalex.org/W2021809202","doi":"https://doi.org/10.1109/hicss.1994.323593","mag":"2021809202"},"language":"en","primary_location":{"id":"doi:10.1109/hicss.1994.323593","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hicss.1994.323593","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94","raw_type":"proceedings-article"},"type":"article","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/A5098544479","display_name":"Bieganski","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bieganski","raw_affiliation_strings":["Computer Science Department, University of Minnesota, USA","University of Minnesota, Minneapolis, MN, US"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Minnesota, USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"University of Minnesota, Minneapolis, MN, US","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056413886","display_name":"Riedl","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210135252","display_name":"University of Minnesota Medical Center","ror":"https://ror.org/03e1ayz78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1309104334","https://openalex.org/I4210135252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Riedl","raw_affiliation_strings":["Medical School, University of Minnesota, USA","University of Minnesota, Minneapolis, MN, US"],"affiliations":[{"raw_affiliation_string":"Medical School, University of Minnesota, USA","institution_ids":["https://openalex.org/I4210135252"]},{"raw_affiliation_string":"University of Minnesota, Minneapolis, MN, US","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098367910","display_name":"Cartis","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cartis","raw_affiliation_strings":["Dept. of Comput. Sci., Minnesota Univ., Minneapolis, MN, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Comput. Sci., Minnesota Univ., Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041504440","display_name":"Retzel","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210135252","display_name":"University of Minnesota Medical Center","ror":"https://ror.org/03e1ayz78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1309104334","https://openalex.org/I4210135252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Retzel","raw_affiliation_strings":["Medical School, University of Minnesota, USA","University of Minnesota, Minneapolis, MN, US"],"affiliations":[{"raw_affiliation_string":"Medical School, University of Minnesota, USA","institution_ids":["https://openalex.org/I4210135252"]},{"raw_affiliation_string":"University of Minnesota, Minneapolis, MN, US","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5098544479"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":null,"apc_paid":null,"fwci":1.74168224,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.8739026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"35","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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":0.9919999837875366,"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/suffix","display_name":"Suffix","score":0.788871169090271},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.7850697040557861},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7380859851837158},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.7374125123023987},{"id":"https://openalex.org/keywords/gestalt-psychology","display_name":"Gestalt psychology","score":0.6169509291648865},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6035179495811462},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5007574558258057},{"id":"https://openalex.org/keywords/generalized-suffix-tree","display_name":"Generalized suffix tree","score":0.46554479002952576},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4652577042579651},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.4332757592201233},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3868412673473358},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3813750445842743},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36228039860725403},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19480198621749878},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17272669076919556},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09986642003059387},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08005240559577942}],"concepts":[{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.788871169090271},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.7850697040557861},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7380859851837158},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7374125123023987},{"id":"https://openalex.org/C27362006","wikidata":"https://www.wikidata.org/wiki/Q272021","display_name":"Gestalt psychology","level":3,"score":0.6169509291648865},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6035179495811462},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5007574558258057},{"id":"https://openalex.org/C118146561","wikidata":"https://www.wikidata.org/wiki/Q5532514","display_name":"Generalized suffix tree","level":4,"score":0.46554479002952576},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4652577042579651},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.4332757592201233},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3868412673473358},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3813750445842743},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36228039860725403},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19480198621749878},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17272669076919556},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09986642003059387},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08005240559577942},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","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/C26760741","wikidata":"https://www.wikidata.org/wiki/Q160402","display_name":"Perception","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/hicss.1994.323593","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hicss.1994.323593","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W166139681","https://openalex.org/W1558365920","https://openalex.org/W1966250735","https://openalex.org/W1969850472","https://openalex.org/W1983265703","https://openalex.org/W1983325631","https://openalex.org/W1987366600","https://openalex.org/W2016219933","https://openalex.org/W2035239012","https://openalex.org/W2035582095","https://openalex.org/W2045067706","https://openalex.org/W2049074555","https://openalex.org/W2049471110","https://openalex.org/W2051256134","https://openalex.org/W2052899946","https://openalex.org/W2063523065","https://openalex.org/W2068519185","https://openalex.org/W2074231493","https://openalex.org/W2085668020","https://openalex.org/W2088156508","https://openalex.org/W2106508890","https://openalex.org/W2112747630","https://openalex.org/W2117175075","https://openalex.org/W2121252285","https://openalex.org/W2135326109","https://openalex.org/W2149202424","https://openalex.org/W2162945593","https://openalex.org/W4210987016","https://openalex.org/W4236327966","https://openalex.org/W4244842753","https://openalex.org/W4246726420","https://openalex.org/W4246917063","https://openalex.org/W4252502986","https://openalex.org/W4253539230","https://openalex.org/W4300796046","https://openalex.org/W4366064364","https://openalex.org/W4401409847"],"related_works":["https://openalex.org/W96331545","https://openalex.org/W1517600056","https://openalex.org/W1575722140","https://openalex.org/W1548907175","https://openalex.org/W2160738675","https://openalex.org/W2036633468","https://openalex.org/W3022556214","https://openalex.org/W4293529780","https://openalex.org/W193772702","https://openalex.org/W2003608043"],"abstract_inverted_index":{"This":[0],"paper":[1],"addresses":[2],"applications":[3,122],"of":[4,22,43,50,77],"suffix":[5,9,23],"trees":[6,10,24],"and":[7,25,41,108],"generalized":[8],"(GSTs)":[11],"to":[12,29,112,115,131],"biological":[13,140],"sequence":[14,31,51,96,127,141],"data":[15,32,52],"analysis.":[16,33],"We":[17,91],"define":[18],"a":[19,93],"basic":[20],"set":[21],"GST":[26,45,56,124],"operations":[27],"needed":[28],"support":[30],"While":[34],"those":[35],"definitions":[36],"are":[37,135],"straightforward,":[38],"the":[39,61,89],"construction":[40],"manipulation":[42],"disk-based":[44],"structures":[46,125],"for":[47,69,126,138],"large":[48],"volumes":[49],"requires":[53],"intricate":[54],"design.":[55],"processing":[57],"is":[58,63],"fast":[59],"because":[60],"structure":[62],"content":[64],"addressable,":[65],"supporting":[66],"efficient":[67],"searches":[68],"all":[70,103],"sequences":[71,80],"that":[72,133],"contain":[73],"particular":[74],"subsequences.":[75],"Instead":[76],"laboriously":[78],"searching":[79],"stored":[81],"as":[82],"arrays,":[83],"we":[84],"search":[85,111],"by":[86],"walking":[87],"down":[88],"tree.":[90],"present":[92],"new":[94],"GST-based":[95],"alignment":[97],"algorithm,":[98],"called":[99],"GESTALT.":[100],"GESTALT":[101],"finds":[102],"exact":[104],"matches":[105],"in":[106],"parallel,":[107],"uses":[109],"best-first":[110],"extend":[113],"them":[114],"produce":[116],"alignments.":[117],"Our":[118],"implementation":[119],"experiences":[120],"with":[121],"using":[123],"analysis":[128],"lead":[129],"us":[130],"conclude":[132],"GSTs":[134],"valuable":[136],"tools":[137],"analyzing":[139],"data.<":[142],"<ETX":[143],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[144],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">&gt;</ETX>":[145]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}