{"id":"https://openalex.org/W1969465720","doi":"https://doi.org/10.1093/nar/gks1265","title":"Dfam: a database of repetitive DNA based on profile hidden Markov models","display_name":"Dfam: a database of repetitive DNA based on profile hidden Markov models","publication_year":2012,"publication_date":"2012-11-30","ids":{"openalex":"https://openalex.org/W1969465720","doi":"https://doi.org/10.1093/nar/gks1265","mag":"1969465720","pmid":"https://pubmed.ncbi.nlm.nih.gov/23203985"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gks1265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks1265","pdf_url":"https://academic.oup.com/nar/article-pdf/41/D1/D70/3714131/gks1265.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/41/D1/D70/3714131/gks1265.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073174813","display_name":"Travis J. Wheeler","orcid":"https://orcid.org/0000-0003-2004-1785"},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Travis J. Wheeler","raw_affiliation_strings":["HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA. wheelert@janelia.hhmi.org","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA. wheelert@janelia.hhmi.org","institution_ids":["https://openalex.org/I195573530"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084167899","display_name":"Jody Clements","orcid":"https://orcid.org/0000-0003-3932-8188"},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jody Clements","raw_affiliation_strings":["HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","institution_ids":["https://openalex.org/I195573530"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020118397","display_name":"Sean R. Eddy","orcid":"https://orcid.org/0000-0001-6676-4706"},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean R. Eddy","raw_affiliation_strings":["HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","institution_ids":["https://openalex.org/I195573530"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063417406","display_name":"Robert Hubley","orcid":"https://orcid.org/0000-0001-9261-3821"},"institutions":[{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Hubley","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA 98109, USA and","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA 98109, USA and","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041634250","display_name":"Thomas A. Jones","orcid":"https://orcid.org/0000-0003-0748-9550"},"institutions":[{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas A. Jones","raw_affiliation_strings":["HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","institution_ids":["https://openalex.org/I195573530"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046140078","display_name":"Jerzy Jurka","orcid":null},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jerzy Jurka","raw_affiliation_strings":["Genetic Information Research Institute, Mountain View, CA 94043, USA","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I171955805"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066827440","display_name":"Arian F. A. Smit","orcid":"https://orcid.org/0000-0003-2088-3165"},"institutions":[{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arian F. A. Smit","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA 98109, USA and","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA 98109, USA and","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5104045098","display_name":"ROBERT FINN","orcid":"https://orcid.org/0000-0001-8626-2148"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I171955805","display_name":"Genetic Information Research Institute","ror":"https://ror.org/01jngdt03","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I171955805"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert D. Finn","raw_affiliation_strings":["HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA"],"affiliations":[{"raw_affiliation_string":"HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA,","institution_ids":["https://openalex.org/I195573530"]},{"raw_affiliation_string":"1HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA, 2Institute for Systems Biology, Seattle, WA 98109, USA and 3Genetic Information Research Institute, Mountain View, CA 94043, USA","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I171955805","https://openalex.org/I3148997608"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5073174813"],"corresponding_institution_ids":["https://openalex.org/I171955805","https://openalex.org/I195573530","https://openalex.org/I3148997608"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":6.0508,"has_fulltext":true,"cited_by_count":317,"citation_normalized_percentile":{"value":0.97245195,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"41","issue":"D1","first_page":"D70","last_page":"D82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"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/annotation","display_name":"Annotation","score":0.7312030792236328},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6999210119247437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5745300054550171},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.5377398133277893},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5105706453323364},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5026772022247314},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.47067365050315857},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45961448550224304},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45522060990333557},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2846800684928894},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10486581921577454},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.10377970337867737}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7312030792236328},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6999210119247437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5745300054550171},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.5377398133277893},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5105706453323364},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5026772022247314},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.47067365050315857},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45961448550224304},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45522060990333557},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2846800684928894},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10486581921577454},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.10377970337867737}],"mesh":[{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gks1265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks1265","pdf_url":"https://academic.oup.com/nar/article-pdf/41/D1/D70/3714131/gks1265.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:23203985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23203985","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.790.4965","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.790.4965","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/d4/8d/gks1265.PMC3531169.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2590268","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3531169","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gks1265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks1265","pdf_url":"https://academic.oup.com/nar/article-pdf/41/D1/D70/3714131/gks1265.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G591728303","display_name":null,"funder_award_id":"Janelia","funder_id":"https://openalex.org/F4320306082","funder_display_name":"Howard Hughes Medical Institute"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1969465720.pdf","grobid_xml":"https://content.openalex.org/works/W1969465720.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1556105006","https://openalex.org/W2009570821","https://openalex.org/W2033049603","https://openalex.org/W2058336694","https://openalex.org/W2071501400","https://openalex.org/W2109293112","https://openalex.org/W2112814753","https://openalex.org/W2130682154","https://openalex.org/W2132926880","https://openalex.org/W2138122982","https://openalex.org/W2141885858","https://openalex.org/W2171975444","https://openalex.org/W4245668478","https://openalex.org/W4320301318","https://openalex.org/W6964227614"],"related_works":["https://openalex.org/W1999129612","https://openalex.org/W2162782320","https://openalex.org/W2059565715","https://openalex.org/W3111061871","https://openalex.org/W4232413416","https://openalex.org/W2009940763","https://openalex.org/W2114034054","https://openalex.org/W2537312848","https://openalex.org/W45826765","https://openalex.org/W1760213857"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,14,94,103,132,159,170,192],"database":[3],"of":[4,17,21,26,28,34,55,96,182,194,221],"repetitive":[5,18],"DNA":[6],"elements,":[7],"called":[8],"Dfam":[9,107,127,157,207],"(http://dfam.janelia.org).":[10],"Many":[11],"genomes":[12],"contain":[13],"large":[15,171],"fraction":[16],"DNA,":[19],"much":[20],"which":[22,117],"is":[23,129,187,208],"made":[24],"up":[25],"remnants":[27],"transposable":[29],"elements":[30],"(TEs).":[31],"Accurate":[32],"annotation":[33,64,73,205],"TEs":[35,56],"enables":[36],"research":[37],"into":[38],"their":[39],"biology":[40],"and":[41,53,65,76,87,143,180,196,204],"can":[42,57],"shed":[43],"light":[44],"on":[45,79,169],"the":[46,123,150,183,219],"evolutionary":[47],"processes":[48],"that":[49],"shape":[50],"genomes.":[51],"Identification":[52],"masking":[54],"also":[58,209],"greatly":[59],"simplify":[60],"many":[61],"downstream":[62],"genome":[63,186],"sequence":[66,80,166],"analysis":[67],"tasks.":[68],"The":[69,189],"commonly":[70],"used":[71,146],"TE":[72,98,114,202],"tools":[74,83,195],"RepeatMasker":[75,142],"Censor":[77],"depend":[78],"homology":[81],"search":[82,154,167],"such":[84],"as":[85,90,92],"cross_match":[86],"BLAST":[88],"variants,":[89],"well":[91],"Repbase,":[93],"collection":[95,193],"known":[97],"families":[99],"each":[100],"represented":[101,130],"by":[102,131],"single":[104],"consensus":[105,165],"sequence.":[106],"contains":[108],"entries":[109,115],"corresponding":[110],"to":[111,199],"all":[112],"Repbase":[113],"for":[116,211],"instances":[118],"have":[119],"been":[120],"found":[121],"in":[122,147,162,213,218],"human":[124,172,185],"genome.":[125],"Each":[126],"entry":[128],"profile":[133],"hidden":[134,151],"Markov":[135,152],"model,":[136],"built":[137],"from":[138],"alignments":[139],"generated":[140],"using":[141],"Repbase.":[144],"When":[145],"conjunction":[148],"with":[149],"model":[153],"tool":[155],"nhmmer,":[156],"produces":[158],"2.9%":[160],"increase":[161],"coverage":[163,181],"over":[164],"methods":[168],"benchmark,":[173],"while":[174],"maintaining":[175],"low":[176],"false":[177],"discovery":[178],"rates,":[179],"full":[184],"54.5%.":[188],"website":[190],"provides":[191],"data":[197],"views":[198],"support":[200],"improved":[201],"curation":[203],"efforts.":[206],"available":[210],"download":[212],"flat":[214],"file":[215],"format":[216],"or":[217],"form":[220],"MySQL":[222],"table":[223],"dumps.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":32},{"year":2024,"cited_by_count":52},{"year":2023,"cited_by_count":43},{"year":2022,"cited_by_count":30},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":22},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":21},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
