{"id":"https://openalex.org/W2089052894","doi":"https://doi.org/10.1142/s0129054105003716","title":"A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS","display_name":"A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS","publication_year":2005,"publication_date":"2005-12-01","ids":{"openalex":"https://openalex.org/W2089052894","doi":"https://doi.org/10.1142/s0129054105003716","mag":"2089052894"},"language":"en","primary_location":{"id":"doi:10.1142/s0129054105003716","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129054105003716","pdf_url":null,"source":{"id":"https://openalex.org/S68047077","display_name":"International Journal of Foundations of Computer Science","issn_l":"0129-0541","issn":["0129-0541","1793-6373"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Foundations of Computer Science","raw_type":"journal-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/A5058155947","display_name":"Costas S. Iliopoulos","orcid":"https://orcid.org/0000-0003-3909-0077"},"institutions":[{"id":"https://openalex.org/I1289762815","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1289762815"]},{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]},{"id":"https://openalex.org/I205640436","display_name":"Curtin University","ror":"https://ror.org/02n415q13","country_code":"AU","type":"education","lineage":["https://openalex.org/I205640436"]}],"countries":["AU","GB"],"is_corresponding":false,"raw_author_name":"COSTAS S. ILIOPOULOS","raw_affiliation_strings":["Dept. Computer Science,  King's College London, London WC2R 2LS, England","School of Computing, Curtin  University of Technology, GPO Box 1987 U, WA, Australia","Dept. Computer Science, King's College London, London WC2R 2LS, England","School of Computing, Curtin University of Technology, GPO Box 1987 U, WA, Australia","The work was partially supported by a NATO grant PST.CLG.977017,  a Marie Curie Fellowship, a Royal Society and a Wellcome Foundation  grant"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Computer Science,  King's College London, London WC2R 2LS, England","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"School of Computing, Curtin  University of Technology, GPO Box 1987 U, WA, Australia","institution_ids":["https://openalex.org/I205640436"]},{"raw_affiliation_string":"Dept. Computer Science, King's College London, London WC2R 2LS, England","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"School of Computing, Curtin University of Technology, GPO Box 1987 U, WA, Australia","institution_ids":["https://openalex.org/I205640436"]},{"raw_affiliation_string":"The work was partially supported by a NATO grant PST.CLG.977017,  a Marie Curie Fellowship, a Royal Society and a Wellcome Foundation  grant","institution_ids":["https://openalex.org/I1289762815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111797562","display_name":"J D A McHugh","orcid":null},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"JAMES MCHUGH","raw_affiliation_strings":["New Jersey Institute of Technology  College of Computing Sciences 323 M.L.King Blvd., University Heights  Newark, NJ 07102-1982, USA","New Jersey Institute of Technology College of Computing Sciences 323 M.L.King Blvd., University Heights Newark, NJ 07102-1982, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Jersey Institute of Technology  College of Computing Sciences 323 M.L.King Blvd., University Heights  Newark, NJ 07102-1982, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"New Jersey Institute of Technology College of Computing Sciences 323 M.L.King Blvd., University Heights Newark, NJ 07102-1982, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012897398","display_name":"Pierre Peterlongo","orcid":"https://orcid.org/0000-0003-0776-6407"},"institutions":[{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"PIERRE PETERLONGO","raw_affiliation_strings":["Institut Gaspard-Monge,  Universit\u00e9 de Marne-la-Vall\u00e9e, Cit\u00e9  Descartes, Champs sur Marne, 77454 Marne-la-Vall\u00e9e  CEDEX 2, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Gaspard-Monge,  Universit\u00e9 de Marne-la-Vall\u00e9e, Cit\u00e9  Descartes, Champs sur Marne, 77454 Marne-la-Vall\u00e9e  CEDEX 2, France","institution_ids":["https://openalex.org/I4210152518"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081785647","display_name":"Nadia Pisanti","orcid":"https://orcid.org/0000-0003-3915-7665"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I4210103285","display_name":"Minist\u00e8re de l'Int\u00e9rieur","ror":"https://ror.org/015jj1011","country_code":"FR","type":"government","lineage":["https://openalex.org/I2799662587","https://openalex.org/I2799681489","https://openalex.org/I2802818602","https://openalex.org/I4210103285","https://openalex.org/I4210136690"]}],"countries":["FR","IT"],"is_corresponding":false,"raw_author_name":"NADIA PISANTI","raw_affiliation_strings":["Department of Computer Science,  University of Pisa, Italy","Department of Computer Science, University of Pisa, Italy","Partially supported by Programme Bioinformatique inter  EPST and the French Ministry of Research through the ACI NIM"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science,  University of Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Partially supported by Programme Bioinformatique inter  EPST and the French Ministry of Research through the ACI NIM","institution_ids":["https://openalex.org/I4210103285"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079957387","display_name":"Wojciech Rytter","orcid":"https://orcid.org/0000-0002-9162-6724"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"WOJCIECH RYTTER","raw_affiliation_strings":["New Jersey Institute of  Technology College of Computing Sciences 323 M.L.King Blvd.,  University Heights Newark, NJ 07102-1982, USA","New Jersey Institute of Technology College of Computing Sciences 323 M.L.King Blvd., University Heights Newark, NJ 07102-1982, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Jersey Institute of  Technology College of Computing Sciences 323 M.L.King Blvd.,  University Heights Newark, NJ 07102-1982, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"New Jersey Institute of Technology College of Computing Sciences 323 M.L.King Blvd., University Heights Newark, NJ 07102-1982, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110531794","display_name":"Marie-France Sagot","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1311060795","display_name":"U.S. National Science Foundation","ror":"https://ror.org/021nxhr62","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"MARIE-FRANCE SAGOT","raw_affiliation_strings":["Inria Rh\u00f4ne-Alpes,  UMR 5558 Biom\u00e9trie et Biologie \u00c9volutive  Universit\u00e9 Claude Bernard, Lyon 1. 43, Bd du 11  novembre 1918 69622 Villeurbanne cedex, France","Partially supported by Programme Bioinformatique inter EPST and  the French Ministry of Research through the ACI NIM, and by Royal  Society, Nato and Wellcome Foundation Grants"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Rh\u00f4ne-Alpes,  UMR 5558 Biom\u00e9trie et Biologie \u00c9volutive  Universit\u00e9 Claude Bernard, Lyon 1. 43, Bd du 11  novembre 1918 69622 Villeurbanne cedex, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I4210135640"]},{"raw_affiliation_string":"Partially supported by Programme Bioinformatique inter EPST and  the French Ministry of Research through the ACI NIM, and by Royal  Society, Nato and Wellcome Foundation Grants","institution_ids":["https://openalex.org/I1311060795"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.8143,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.95666309,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"06","first_page":"1145","last_page":"1154"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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":0.9998000264167786,"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/T11567","display_name":"semigroups and automata theory","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10601","display_name":"Handwritten Text Recognition Techniques","score":0.9739000201225281,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/alphabet","display_name":"Alphabet","score":0.6282256841659546},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5925052165985107},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.5503824353218079},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.5370157957077026},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4926488995552063},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4365732669830322},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3514193296432495}],"concepts":[{"id":"https://openalex.org/C112876837","wikidata":"https://www.wikidata.org/wiki/Q837518","display_name":"Alphabet","level":2,"score":0.6282256841659546},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5925052165985107},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.5503824353218079},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.5370157957077026},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4926488995552063},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4365732669830322},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3514193296432495},{"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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1142/s0129054105003716","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129054105003716","pdf_url":null,"source":{"id":"https://openalex.org/S68047077","display_name":"International Journal of Foundations of Computer Science","issn_l":"0129-0541","issn":["0129-0541","1793-6373"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Foundations of Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:arpi.unipi.it:11568/892391","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/892391","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:arpi.unipi.it:11568/91803","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/91803","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:kclpure.kcl.ac.uk:publications/62b6ba3c-82b8-4cbe-90c4-b9f7d750dfe1","is_oa":false,"landing_page_url":"https://kclpure.kcl.ac.uk/portal/en/publications/62b6ba3c-82b8-4cbe-90c4-b9f7d750dfe1","pdf_url":null,"source":{"id":"https://openalex.org/S4306400216","display_name":"Research Portal (King's College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I183935753","host_organization_name":"King's College London","host_organization_lineage":["https://openalex.org/I183935753"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Iliopoulos, C S, McHugh, J, Peterlongo, P, Pisanti, N, Rytter, W & Sagot, M F 2005, 'A first approach to finding common motifs with gaps', INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, vol. 16, no. 6, N/A, pp. 1145 - 1154. https://doi.org/10.1142/S0129054105003716","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.7599999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1532280479","https://openalex.org/W1606755952","https://openalex.org/W2021809202","https://openalex.org/W2107079154","https://openalex.org/W2611477341"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2074481494","https://openalex.org/W2808006995","https://openalex.org/W4250156143","https://openalex.org/W4247156967","https://openalex.org/W2544423928","https://openalex.org/W2189341500","https://openalex.org/W1589381382","https://openalex.org/W961142965"],"abstract_inverted_index":{"We":[0],"present":[1],"three":[2,18],"linear":[3,59],"algorithms":[4],"for":[5],"as":[6],"many":[7],"formulations":[8],"of":[9,12,20,34,39,77,86,90,98,104,126],"the":[10,21,32,35,40,44,53,65,78,91,99,102,127],"problem":[11,22,128],"finding":[13],"motifs":[14],"with":[15,62],"gaps.":[16,36],"The":[17,37,68,95,111],"versions":[19],"are":[23],"distinct":[24],"in":[25,114,133],"that":[26,80,118],"they":[27],"assume":[28],"different":[29],"constraints":[30],"on":[31,74],"size":[33],"outline":[38],"algorithm":[41,100,112],"is":[42,48,72,113],"always":[43],"same,":[45],"although":[46],"this":[47,134],"adapted":[49],"each":[50],"time":[51,60],"to":[52,64,107,123],"specific":[54],"problem,":[55],"while":[56],"maintaining":[57],"a":[58,75,82],"complexity":[61,97],"respect":[63],"input":[66,93],"size.":[67],"approach":[69],"we":[70],"suggest":[71],"based":[73],"re-writing":[76],"text":[79],"uses":[81],"new":[83],"alphabet":[84],"made":[85],"labels":[87],"representing":[88],"words":[89],"original":[92],"text.":[94],"computational":[96],"allows":[101],"use":[103],"it":[105,119],"also":[106],"find":[108],"long":[109],"motifs.":[110],"fact":[115],"general":[116],"enough":[117],"could":[120],"be":[121],"applied":[122],"several":[124],"variants":[125],"other":[129],"than":[130],"those":[131],"suggested":[132],"paper.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
