{"id":"https://openalex.org/W2172219143","doi":"https://doi.org/10.1177/0165551506062329","title":"An efficient DNA sequence searching method using position specific weighting scheme","display_name":"An efficient DNA sequence searching method using position specific weighting scheme","publication_year":2006,"publication_date":"2006-03-21","ids":{"openalex":"https://openalex.org/W2172219143","doi":"https://doi.org/10.1177/0165551506062329","mag":"2172219143"},"language":"en","primary_location":{"id":"doi:10.1177/0165551506062329","is_oa":true,"landing_page_url":"https://doi.org/10.1177/0165551506062329","pdf_url":"https://journals.sagepub.com/doi/pdf/10.1177/0165551506062329?download=true","source":{"id":"https://openalex.org/S68913162","display_name":"Journal of Information Science","issn_l":"0165-5515","issn":["0165-5515","1741-6485"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://journals.sagepub.com/doi/pdf/10.1177/0165551506062329?download=true","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102955746","display_name":"Woocheol Kim","orcid":"https://orcid.org/0000-0002-0865-846X"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Woo-Cheol Kim","raw_affiliation_strings":["Department of Computer Science , Yonsei University , Korea","Dept. of Computer Science, Yonsei Univ., Korea#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , Yonsei University , Korea","institution_ids":["https://openalex.org/I193775966"]},{"raw_affiliation_string":"Dept. of Computer Science, Yonsei Univ., Korea#TAB#","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100322282","display_name":"Sanghyun Park","orcid":"https://orcid.org/0000-0003-3579-3912"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sanghyun Park","raw_affiliation_strings":["Department of Computer Science , Yonsei University , Korea","College of Information and Communications, Hanyang Univ., Korea#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , Yonsei University , Korea","institution_ids":["https://openalex.org/I193775966"]},{"raw_affiliation_string":"College of Information and Communications, Hanyang Univ., Korea#TAB#","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068972746","display_name":"Jung-Im Won","orcid":"https://orcid.org/0000-0003-3591-7735"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jung-Im Won","raw_affiliation_strings":["Department of Computer Science, Yonsei University, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yonsei University, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100656150","display_name":"Sang\u2010Wook Kim","orcid":"https://orcid.org/0000-0002-6345-9084"},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sang-Wook Kim","raw_affiliation_strings":["College of Information and Communications, Hanyang University, Korea","College of Information and Communications, Hanyang Univ., Korea#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information and Communications, Hanyang University, Korea","institution_ids":["https://openalex.org/I4575257"]},{"raw_affiliation_string":"College of Information and Communications, Hanyang Univ., Korea#TAB#","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027497636","display_name":"Jeehee Yoon","orcid":"https://orcid.org/0000-0002-4327-3135"},"institutions":[{"id":"https://openalex.org/I146824383","display_name":"Hallym University","ror":"https://ror.org/03sbhge02","country_code":"KR","type":"education","lineage":["https://openalex.org/I146824383"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jee-Hee Yoon","raw_affiliation_strings":["Division of Information Engineering and Telecommunications, Hallym                         University, Korea","Division of Information Engineering and Telecommunications, Hallym University, Korea#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Information Engineering and Telecommunications, Hallym                         University, Korea","institution_ids":["https://openalex.org/I146824383"]},{"raw_affiliation_string":"Division of Information Engineering and Telecommunications, Hallym University, Korea#TAB#","institution_ids":["https://openalex.org/I146824383"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3867,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.85623278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"32","issue":"2","first_page":"176","last_page":"190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9918000102043152,"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/T12029","display_name":"DNA and Biological Computing","score":0.9904000163078308,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.8144431114196777},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6846106648445129},{"id":"https://openalex.org/keywords/rectangle","display_name":"Rectangle","score":0.6674026250839233},{"id":"https://openalex.org/keywords/sliding-window-protocol","display_name":"Sliding window protocol","score":0.6041359901428223},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5984190106391907},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.5919662714004517},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4984314441680908},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4941897690296173},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4819890856742859},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3571770191192627},{"id":"https://openalex.org/keywords/window","display_name":"Window (computing)","score":0.35224902629852295},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3083322048187256},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23463812470436096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1384413242340088},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09392580389976501}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.8144431114196777},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6846106648445129},{"id":"https://openalex.org/C2781302577","wikidata":"https://www.wikidata.org/wiki/Q209","display_name":"Rectangle","level":2,"score":0.6674026250839233},{"id":"https://openalex.org/C102392041","wikidata":"https://www.wikidata.org/wiki/Q592860","display_name":"Sliding window protocol","level":3,"score":0.6041359901428223},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5984190106391907},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.5919662714004517},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4984314441680908},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4941897690296173},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4819890856742859},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3571770191192627},{"id":"https://openalex.org/C2778751112","wikidata":"https://www.wikidata.org/wiki/Q835016","display_name":"Window (computing)","level":2,"score":0.35224902629852295},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3083322048187256},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23463812470436096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1384413242340088},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09392580389976501},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/0165551506062329","is_oa":true,"landing_page_url":"https://doi.org/10.1177/0165551506062329","pdf_url":"https://journals.sagepub.com/doi/pdf/10.1177/0165551506062329?download=true","source":{"id":"https://openalex.org/S68913162","display_name":"Journal of Information Science","issn_l":"0165-5515","issn":["0165-5515","1741-6485"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information Science","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1177/0165551506062329","is_oa":true,"landing_page_url":"https://doi.org/10.1177/0165551506062329","pdf_url":"https://journals.sagepub.com/doi/pdf/10.1177/0165551506062329?download=true","source":{"id":"https://openalex.org/S68913162","display_name":"Journal of Information Science","issn_l":"0165-5515","issn":["0165-5515","1741-6485"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321191","display_name":"Jeju National University","ror":"https://ror.org/05hnb4n85"},{"id":"https://openalex.org/F4320322348","display_name":"Korea Science and Engineering Foundation","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2172219143.pdf","grobid_xml":"https://content.openalex.org/works/W2172219143.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1492127831","https://openalex.org/W1499049447","https://openalex.org/W1504417041","https://openalex.org/W1529615245","https://openalex.org/W1812430439","https://openalex.org/W1985108724","https://openalex.org/W1986324942","https://openalex.org/W1990061958","https://openalex.org/W2034474362","https://openalex.org/W2055043387","https://openalex.org/W2062393514","https://openalex.org/W2068421750","https://openalex.org/W2085218027","https://openalex.org/W2087064593","https://openalex.org/W2099964107","https://openalex.org/W2103014446","https://openalex.org/W2103934658","https://openalex.org/W2116509046","https://openalex.org/W2118269922","https://openalex.org/W2134826720","https://openalex.org/W2158714788","https://openalex.org/W2158874082","https://openalex.org/W2238624099","https://openalex.org/W2610179052","https://openalex.org/W3137072739"],"related_works":["https://openalex.org/W2242098268","https://openalex.org/W4244945894","https://openalex.org/W2180954594","https://openalex.org/W4224881918","https://openalex.org/W2760515006","https://openalex.org/W1987609185","https://openalex.org/W2003462717","https://openalex.org/W2183169553","https://openalex.org/W2995646754","https://openalex.org/W3014558862"],"abstract_inverted_index":{"Exact":[0],"match":[1,4],"queries,":[2,5,170],"wildcard":[3,166],"and":[6,26,38,59,122,152,168],"k":[7],"mismatch":[8],"queries":[9],"are":[10],"widely":[11],"used":[12],"in":[13,107,162],"various":[14],"molecular":[15],"biology":[16],"applications":[17],"including":[18],"the":[19,65,84,124,127,131,142,159],"searching":[20],"of":[21,55,68,76,94,155],"ESTs":[22],"(Expressed":[23],"Sequence":[24],"Tags)":[25],"DNA":[27,57],"transcription":[28],"factors.":[29],"In":[30],"this":[31],"paper,":[32],"we":[33],"suggest":[34],"an":[35],"efficient":[36],"indexing":[37,45,108],"processing":[39,112],"mechanism":[40],"for":[41,126],"such":[42,82],"queries.":[43],"Our":[44,110],"method":[46,113],"places":[47],"a":[48,56,74,79,89,95,104,115,119],"sliding":[49],"window":[50],"at":[51,146],"every":[52],"possible":[53],"location":[54],"sequence":[58,117],"extracts":[60],"its":[61],"signature":[62],"by":[63,87],"considering":[64],"occurrence":[66],"frequency":[67],"each":[69,92],"nucleotide.":[70],"It":[71],"then":[72],"stores":[73],"set":[75],"signatures":[77,99,128],"using":[78],"multi-dimensional":[80,120],"index":[81,125],"as":[83],"R*-tree.":[85],"Also,":[86],"assigning":[88],"weight":[90],"to":[91],"position":[93],"window,":[96],"it":[97],"prevents":[98],"from":[100],"being":[101],"concentrated":[102],"around":[103],"few":[105],"spots":[106],"space.":[109],"query":[111,116],"converts":[114],"into":[118],"rectangle":[121],"searches":[123],"overlapping":[129],"with":[130,134],"rectangle.":[132],"Experiments":[133],"real":[135],"biological":[136],"data":[137],"sets":[138],"have":[139],"revealed":[140],"that":[141],"proposed":[143],"approach":[144],"is":[145],"least":[147],"4.4":[148],"times,":[149,151],"2.1":[150],"several":[153],"orders":[154],"magnitude":[156],"faster":[157],"than":[158],"previous":[160],"one":[161],"performing":[163],"exact":[164],"match,":[165,167],"k-mismatch":[169],"respectively.":[171]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-25T06:16:34.145877","created_date":"2025-10-10T00:00:00"}
