{"id":"https://openalex.org/W2148315173","doi":"https://doi.org/10.1109/cec.2008.4631146","title":"N-SAMSAM : A simple and faster algorithm for solving approximate matching in DNA sequences","display_name":"N-SAMSAM : A simple and faster algorithm for solving approximate matching in DNA sequences","publication_year":2008,"publication_date":"2008-06-01","ids":{"openalex":"https://openalex.org/W2148315173","doi":"https://doi.org/10.1109/cec.2008.4631146","mag":"2148315173"},"language":"en","primary_location":{"id":"doi:10.1109/cec.2008.4631146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2008.4631146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence)","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/A5053483219","display_name":"Bing Ni","orcid":"https://orcid.org/0000-0002-4297-5346"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bing Ni","raw_affiliation_strings":["Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064272204","display_name":"Ming Hung Wong","orcid":"https://orcid.org/0009-0002-6077-4369"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"M.H. Wong","raw_affiliation_strings":["Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082233800","display_name":"Kwong\u2010Sak Leung","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"K.S. Leung","raw_affiliation_strings":["Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chinese University of Hong Kong, New Territories, Hong Kong, China","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053483219"],"corresponding_institution_ids":["https://openalex.org/I177725633"],"apc_list":null,"apc_paid":null,"fwci":1.1441,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.84985302,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"8","issue":null,"first_page":"2592","last_page":"2598"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":1.0,"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":1.0,"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":0.9941999912261963,"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":0.9886999726295471,"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/substring","display_name":"Substring","score":0.9726593494415283},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.7839488983154297},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7465580105781555},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6421456336975098},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.5903092622756958},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.5819039344787598},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.5776742696762085},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5498356223106384},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.5282706022262573},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.48503369092941284},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.4700393080711365},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.46159788966178894},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4544955790042877},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.45247355103492737},{"id":"https://openalex.org/keywords/trie","display_name":"Trie","score":0.43179476261138916},{"id":"https://openalex.org/keywords/approximate-string-matching","display_name":"Approximate string matching","score":0.4221600592136383},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24609321355819702},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13806745409965515},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.0675194263458252}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.9726593494415283},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7839488983154297},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7465580105781555},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6421456336975098},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.5903092622756958},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.5819039344787598},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.5776742696762085},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5498356223106384},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.5282706022262573},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.48503369092941284},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.4700393080711365},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.46159788966178894},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4544955790042877},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.45247355103492737},{"id":"https://openalex.org/C190290938","wikidata":"https://www.wikidata.org/wiki/Q387015","display_name":"Trie","level":3,"score":0.43179476261138916},{"id":"https://openalex.org/C32610155","wikidata":"https://www.wikidata.org/wiki/Q1798621","display_name":"Approximate string matching","level":3,"score":0.4221600592136383},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24609321355819702},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13806745409965515},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0675194263458252},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cec.2008.4631146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2008.4631146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence)","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/W185052921","https://openalex.org/W938539187","https://openalex.org/W1485847476","https://openalex.org/W1647671624","https://openalex.org/W1980073965","https://openalex.org/W1992748956","https://openalex.org/W2001496424","https://openalex.org/W2021809202","https://openalex.org/W2030178036","https://openalex.org/W2034767282","https://openalex.org/W2045821558","https://openalex.org/W2059513841","https://openalex.org/W2096210973","https://openalex.org/W2112814753","https://openalex.org/W2121252285","https://openalex.org/W2153127576","https://openalex.org/W2158874082","https://openalex.org/W2342204193","https://openalex.org/W2533248932","https://openalex.org/W2610179052","https://openalex.org/W6636915900"],"related_works":["https://openalex.org/W1593730394","https://openalex.org/W1568850903","https://openalex.org/W2736693933","https://openalex.org/W2124852384","https://openalex.org/W2485439294","https://openalex.org/W75168880","https://openalex.org/W4379644220","https://openalex.org/W3022344494","https://openalex.org/W2560606564","https://openalex.org/W3125798661"],"abstract_inverted_index":{"This":[0],"work":[1],"proposes":[2],"a":[3,11],"novel":[4],"algorithm":[5,20,77,103,121,136,150,184],"to":[6,78,128],"do":[7],"approximate":[8],"matching":[9,117],"in":[10,21,81,84,175,201],"database":[12],"consisting":[13],"of":[14,38,43,53,61,101,108,119,134,148,164,171,193],"multiple":[15],"sequences.":[16],"We":[17,74,125,144,167,188],"apply":[18,79],"Agrep":[19,80,161],"an":[22,76],"indexing":[23,65],"structure,":[24],"the":[25,36,45,54,62,69,82,86,92,99,109,116,132,138,146,152,156,179,191],"r-cut":[26],"numerical":[27],"substring":[28],"array":[29],"(r-NSA).":[30],"The":[31,41,50],"structure":[32],"basically":[33],"indexes":[34],"all":[35],"substrings":[37,87,94],"length":[39],"r.":[40],"advantage":[42],"using":[44],"r-NSA":[46,55],"is":[47,56,104,122],"two-fold:":[48],"(1)":[49],"space":[51],"requirement":[52],"much":[57],"smaller":[58,105],"than":[59,106],"that":[60,107,163,182],"other":[63],"existing":[64],"structures,":[66],"such":[67],"as":[68,151],"generalized":[70],"suffix":[71],"tree.":[72],"(2)":[73],"propose":[75],"r-NSA,":[83],"which":[85],"are":[88,95],"processed":[89,96],"sequentially.":[90],"Since":[91],"common":[93],"only":[97],"once,":[98],"cost":[100],"our":[102,120,135,149,165,176,183],"full":[110,139,157],"scanning":[111,140,158],"search":[112,141,159],"by":[113,142,155,160],"Agrep.":[114,143],"Consequently,":[115],"time":[118,153],"also":[123,189],"reduced.":[124],"design":[126],"experiments":[127],"validate":[129],"and":[130,178,197],"compare":[131],"performance":[133],"against":[137],"define":[145],"speed-up":[147,192],"required":[154],"over":[162],"algorithm.":[166],"use":[168],"eight":[169],"sets":[170],"real":[172],"DNA":[173],"sequences":[174],"experiments,":[177],"results":[180],"show":[181],"achieves":[185],"significant":[186],"speed-up.":[187],"investigate":[190],"difference":[194],"data":[195],"sets,":[196],"analyze":[198],"their":[199],"differences":[200],"detail.":[202]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}