{"id":"https://openalex.org/W4234717156","doi":"https://doi.org/10.1109/csb.2004.1332461","title":"Repeatassembler: a package for annotation of full-length repetitive DNA sequences in fungal genomes","display_name":"Repeatassembler: a package for annotation of full-length repetitive DNA sequences in fungal genomes","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4234717156","doi":"https://doi.org/10.1109/csb.2004.1332461"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332461","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332461","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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/A5083499270","display_name":"M. L.Farman","orcid":null},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]},{"id":"https://openalex.org/I4210151202","display_name":"Plant (United States)","ror":"https://ror.org/05g223j58","country_code":"US","type":"company","lineage":["https://openalex.org/I4210151202"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. L.Farman","raw_affiliation_strings":["Department of Plant Pathology, University of Kentucky, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, University of Kentucky, USA","institution_ids":["https://openalex.org/I143302722","https://openalex.org/I4210151202"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058444936","display_name":"J.W. Gilkerson","orcid":null},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J.W. Gilkerson","raw_affiliation_strings":["Department of Computer Science, University of Kentucky, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Kentucky, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083145635","display_name":"J.W. Jaromczyk","orcid":null},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J.W. Jaromczyk","raw_affiliation_strings":["Department of Computer Science, University of Kentucky, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Kentucky, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088805687","display_name":"C. Staben","orcid":null},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Staben","raw_affiliation_strings":["Department of Biology, University of Kentucky, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Kentucky, USA","institution_ids":["https://openalex.org/I143302722"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.42118227,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"446","last_page":"449"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12668","display_name":"Yeasts and Rust Fungi Studies","score":0.9818000197410583,"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":0.6801767349243164},{"id":"https://openalex.org/keywords/repeated-sequence","display_name":"Repeated sequence","score":0.6572157740592957},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5568846464157104},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5546782612800598},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5307263135910034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48809707164764404},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.4853062033653259},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4831118583679199},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4798107445240021},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.46403929591178894},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.454324871301651},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4260391592979431},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40157413482666016},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3783435821533203},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11957067251205444},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10840126872062683}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6801767349243164},{"id":"https://openalex.org/C169802333","wikidata":"https://www.wikidata.org/wiki/Q424473","display_name":"Repeated sequence","level":4,"score":0.6572157740592957},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5568846464157104},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5546782612800598},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5307263135910034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48809707164764404},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4853062033653259},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4831118583679199},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4798107445240021},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.46403929591178894},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.454324871301651},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4260391592979431},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40157413482666016},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3783435821533203},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11957067251205444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10840126872062683}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2004.1332461","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332461","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.550000011920929}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310177","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":2,"referenced_works":["https://openalex.org/W2115999122","https://openalex.org/W2151899848"],"related_works":["https://openalex.org/W1565527690","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2353729507","https://openalex.org/W4318240630","https://openalex.org/W2350466590","https://openalex.org/W1542620732","https://openalex.org/W3031625301","https://openalex.org/W4308713831","https://openalex.org/W4386771068"],"abstract_inverted_index":{"REPEATASSEMBLER":[0,72,105],"aims":[1],"to":[2,79],"automate":[3],"the":[4,15,24,40,64,67,95,103],"identification":[5],"of":[6,42,69,90],"full-length":[7,96,114],"consensus":[8,97],"sequences":[9,76,109],"for":[10,99,116],"repetitive":[11,83,108],"DNA":[12],"fragments":[13],"or":[14],"genetic":[16],"material":[17],"that":[18,110],"is":[19,54,62],"repeated":[20],"many":[21],"times":[22],"throughout":[23],"genome":[25],"(so-called":[26],"repeats).":[27],"Although":[28],"there":[29],"are":[30],"packages":[31],"with":[32,112],"similar":[33],"objectives,":[34],"e.g.":[35],"RECON,":[36],"none":[37],"fully":[38],"meets":[39],"needs":[41],"researchers":[43],"in":[44,102],"comparative":[45],"genomics.":[46],"Joining":[47],"short":[48],"repeating":[49],"elements":[50],"into":[51],"fall-length":[52],"repeats":[53,92,115],"particularly":[55],"intricate":[56],"and":[57,66,93],"handling":[58],"this":[59],"task":[60],"properly":[61],"both":[63],"goal":[65],"strength":[68],"our":[70],"solution.":[71],"analyzes":[73],"as":[74,77],"few":[75],"possible":[78],"screen":[80],"out":[81],"all":[82],"sequences.":[84],"Then":[85],"it":[86],"builds":[87],"a":[88],"set":[89],"non-redundant":[91],"reports":[94],"sequence":[98],"each":[100],"element":[101],"set.":[104],"consistently":[106],"delivers":[107],"agree":[111],"known":[113],"several":[117],"fungal":[118],"genomes.":[119]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}