{"id":"https://openalex.org/W2105459732","doi":"https://doi.org/10.1093/bioinformatics/btf843","title":"FORRepeats: detects repeats on entire chromosomes and between genomes","display_name":"FORRepeats: detects repeats on entire chromosomes and between genomes","publication_year":2003,"publication_date":"2003-02-12","ids":{"openalex":"https://openalex.org/W2105459732","doi":"https://doi.org/10.1093/bioinformatics/btf843","mag":"2105459732","pmid":"https://pubmed.ncbi.nlm.nih.gov/12584116"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btf843","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf843","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/319/48903710/bioinformatics_19_3_319.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/319/48903710/bioinformatics_19_3_319.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066757544","display_name":"Arnaud Lefebvre","orcid":"https://orcid.org/0000-0001-9631-2292"},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A. Lefebvre","raw_affiliation_strings":["ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052475314","display_name":"Thierry Lecroq","orcid":"https://orcid.org/0000-0002-1900-3397"},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"T. Lecroq","raw_affiliation_strings":["ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065843661","display_name":"H\u00e9l\u00e8ne Dauchel","orcid":"https://orcid.org/0000-0003-3156-9737"},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"H. Dauchel","raw_affiliation_strings":["ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063045355","display_name":"Jo\u00ebl Alexandre","orcid":null},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J. Alexandre","raw_affiliation_strings":["ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ABISS - Universit\u00e9 de Rouen, 76821 Mont Saint-Aignan Cedex, France","institution_ids":["https://openalex.org/I62396329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I62396329"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6225,"has_fulltext":false,"cited_by_count":72,"citation_normalized_percentile":{"value":0.90005191,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"3","first_page":"319","last_page":"326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.28949999809265137,"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":0.28949999809265137,"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":0.27320000529289246,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.16930000483989716,"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/genome","display_name":"Genome","score":0.7785095572471619},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5600063800811768},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5382947325706482},{"id":"https://openalex.org/keywords/oracle","display_name":"Oracle","score":0.5197001099586487},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.517094612121582},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48762574791908264},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.4313158690929413},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4309561252593994},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39270317554473877},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3863145709037781},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.365961492061615},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34643590450286865},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3409402370452881},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23723703622817993},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13436099886894226}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7785095572471619},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5600063800811768},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5382947325706482},{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.5197001099586487},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.517094612121582},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48762574791908264},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.4313158690929413},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4309561252593994},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39270317554473877},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3863145709037781},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.365961492061615},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34643590450286865},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3409402370452881},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23723703622817993},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13436099886894226},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032461","descriptor_name":"Chromosomes, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D032461","descriptor_name":"Chromosomes, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D032461","descriptor_name":"Chromosomes, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btf843","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf843","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/319/48903710/bioinformatics_19_3_319.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:12584116","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12584116","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btf843","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf843","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/319/48903710/bioinformatics_19_3_319.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105459732.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1595313252","https://openalex.org/W1597644352","https://openalex.org/W1924486564","https://openalex.org/W2002027062","https://openalex.org/W2004954279","https://openalex.org/W2034617842","https://openalex.org/W2042507891","https://openalex.org/W2055666215","https://openalex.org/W2109628984","https://openalex.org/W2121252285","https://openalex.org/W2130043776","https://openalex.org/W2141524685","https://openalex.org/W2142744236","https://openalex.org/W2146611007","https://openalex.org/W2148968778","https://openalex.org/W2152331922","https://openalex.org/W2155550908","https://openalex.org/W2158714788","https://openalex.org/W2159077216","https://openalex.org/W2315995143","https://openalex.org/W2915880292"],"related_works":["https://openalex.org/W4315796789","https://openalex.org/W2521866209","https://openalex.org/W3023271652","https://openalex.org/W2101115907","https://openalex.org/W4211093350","https://openalex.org/W119390381","https://openalex.org/W1976142521","https://openalex.org/W4225858648","https://openalex.org/W4383032973","https://openalex.org/W1538818782"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"more":[2,4],"and":[3,20,82,128,139,147,158],"whole":[5],"genomes":[6,26],"are":[7],"available,":[8],"there":[9],"is":[10,32,41,98,145],"a":[11,92,101],"need":[12],"for":[13],"new":[14,29],"methods":[15],"to":[16,27,35,43,51,154,159],"compare":[17,36,44],"large":[18,47,55,117],"sequences":[19,56,163],"transfer":[21],"biological":[22],"knowledge":[23],"from":[24],"annotated":[25],"related":[28,46,87],"ones.":[30],"BLAST":[31,138],"not":[33],"suitable":[34],"multimegabase":[37],"DNA":[38,162],"sequences.":[39,48,118],"MegaBLAST":[40],"designed":[42],"closely":[45],"Some":[49],"tools":[50],"detect":[52,160],"repeats":[53,81,115,127],"in":[54,74,116,120,164],"have":[57,68],"already":[58],"been":[59],"developed":[60],"such":[61],"as":[62],"MUMmer":[63,83],"or":[64,70],"REPuter.":[65,140],"They":[66],"also":[67],"time":[69],"space":[71,148],"restrictions.":[72],"Moreover,":[73],"terms":[75],"of":[76,168],"applications,":[77],"REPuter":[78],"only":[79],"computes":[80,125],"works":[84],"better":[85],"with":[86,137],"genomes.":[88],"RESULTS:":[89],"We":[90,132,150],"present":[91],"heuristic":[93],"method,":[94],"named":[95],"FORRepeats,":[96],"which":[97],"based":[99],"on":[100],"novel":[102],"data":[103],"structure":[104],"called":[105],"factor":[106],"oracle.":[107],"In":[108],"the":[109,121,165,169],"first":[110],"step":[111],"it":[112,124,144],"detects":[113],"exact":[114],"Then,":[119],"second":[122],"step,":[123],"approximate":[126],"performs":[129],"pairwise":[130],"comparison.":[131],"compared":[133],"its":[134],"computational":[135],"characteristics":[136],"Results":[141],"demonstrate":[142],"that":[143],"fast":[146],"economical.":[149],"show":[151],"FORRepeats":[152],"ability":[153],"perform":[155],"intra-genomic":[156],"comparison":[157],"repeated":[161],"complete":[166],"genome":[167],"model":[170],"plant":[171],"Arabidopsis":[172],"thaliana.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}