{"id":"https://openalex.org/W2943174821","doi":"https://doi.org/10.1093/nar/gkz329","title":"MyDGR: a server for identification and characterization of diversity-generating retroelements","display_name":"MyDGR: a server for identification and characterization of diversity-generating retroelements","publication_year":2019,"publication_date":"2019-04-23","ids":{"openalex":"https://openalex.org/W2943174821","doi":"https://doi.org/10.1093/nar/gkz329","mag":"2943174821","pmid":"https://pubmed.ncbi.nlm.nih.gov/31049585"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz329","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W289/28879626/gkz329.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/47/W1/W289/28879626/gkz329.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075639893","display_name":"Fatemeh Sharifi","orcid":"https://orcid.org/0000-0001-6007-5993"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fatemeh Sharifi","raw_affiliation_strings":["School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082620694","display_name":"Yuzhen Ye","orcid":"https://orcid.org/0000-0003-3707-3185"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuzhen Ye","raw_affiliation_strings":["School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082620694"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.3671,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.80933354,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"47","issue":"W1","first_page":"W289","last_page":"W294"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/biology","display_name":"Biology","score":0.7900123596191406},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6832525134086609},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6142172813415527},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5652171969413757},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5563406944274902},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5512696504592896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4778142273426056},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36549848318099976},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3594748377799988},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34603655338287354},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22174298763275146}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7900123596191406},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6832525134086609},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6142172813415527},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5652171969413757},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5563406944274902},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5512696504592896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4778142273426056},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36549848318099976},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3594748377799988},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34603655338287354},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22174298763275146},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D012194","descriptor_name":"RNA-Directed DNA Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012194","descriptor_name":"RNA-Directed DNA Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012194","descriptor_name":"RNA-Directed DNA Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"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":"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":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkz329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz329","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W289/28879626/gkz329.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31049585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31049585","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:europepmc.org:5577315","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602519","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz329","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W289/28879626/gkz329.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G294978622","display_name":null,"funder_award_id":"DBI-1262588","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G6117829801","display_name":null,"funder_award_id":"1R01AI108888","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1967516224","https://openalex.org/W1967886452","https://openalex.org/W1977621080","https://openalex.org/W1982536924","https://openalex.org/W1989021204","https://openalex.org/W2019885489","https://openalex.org/W2021636529","https://openalex.org/W2028577792","https://openalex.org/W2037993016","https://openalex.org/W2047794361","https://openalex.org/W2061617125","https://openalex.org/W2064928476","https://openalex.org/W2069689025","https://openalex.org/W2072904262","https://openalex.org/W2108087602","https://openalex.org/W2117583060","https://openalex.org/W2128081788","https://openalex.org/W2128769815","https://openalex.org/W2129448726","https://openalex.org/W2131415145","https://openalex.org/W2138122982","https://openalex.org/W2142678478","https://openalex.org/W2166123725","https://openalex.org/W2604389286","https://openalex.org/W2769034238","https://openalex.org/W2801635012","https://openalex.org/W2892990496","https://openalex.org/W2895938591","https://openalex.org/W2901674809","https://openalex.org/W2951988846"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"MyDGR":[0,94],"is":[1,20,81],"a":[2,28,109,114,117,156,187],"web":[3,73,86],"server":[4,74],"providing":[5,146],"integrated":[6],"prediction":[7],"and":[8,102,120,126,139,186],"visualization":[9],"of":[10,26,35,77,108,159,191],"Diversity-Generating":[11],"Retroelements":[12],"(DGR)":[13],"systems":[14,39,178],"in":[15,54,99,180],"query":[16,96],"nucleotide":[17,97],"sequences.":[18],"It":[19],"built":[21],"upon":[22],"an":[23],"enhanced":[24],"version":[25],"DGRscan,":[27],"tool":[29],"we":[30],"previously":[31],"developed":[32],"for":[33,75,152,162],"identification":[34],"DGR":[36,38,78,111,168,177],"systems.":[37,169],"are":[40],"remarkable":[41],"genetic":[42],"elements":[43],"that":[44],"use":[45],"error-prone":[46],"reverse":[47,115],"transcriptases":[48],"to":[49,62,145,164],"generate":[50],"vast":[51],"sequence":[52],"variants":[53],"specific":[55],"target":[56,141],"genes,":[57],"which":[58],"have":[59],"been":[60],"shown":[61],"benefit":[63],"their":[64,127],"hosts":[65],"(bacteria,":[66],"archaea":[67],"or":[68,136],"phages).":[69],"As":[70],"the":[71,85,105,147,160,166],"first":[72],"annotation":[76],"systems,":[79],"myDGR":[80,154],"freely":[82],"available":[83,182],"on":[84],"at":[87],"http://omics.informatics.indiana.edu/myDGR":[88],"with":[89],"all":[90,104],"major":[91],"browsers":[92],"supported.":[93],"accepts":[95],"sequences":[98,192],"FASTA":[100],"format,":[101],"outputs":[103],"important":[106],"features":[107],"predicted":[110,167],"system,":[112],"including":[113],"transcriptase,":[116],"template":[118],"repeat":[119],"one":[121],"(or":[122],"more)":[123],"variable":[124],"repeats":[125],"alignment":[128],"featuring":[129],"A-to-N":[130],"(N":[131],"can":[132,171],"be":[133],"C,":[134],"T":[135],"G)":[137],"substitutions,":[138],"VR-containing":[140],"gene(s).":[142],"In":[143],"addition":[144],"results":[148,161],"as":[149],"text":[150],"files":[151],"download,":[153],"generates":[155],"visual":[157],"summary":[158],"users":[163],"explore":[165],"Users":[170],"also":[172],"directly":[173],"access":[174],"pre-calculated,":[175],"putative":[176],"identified":[179],"currently":[181],"reference":[183],"bacterial":[184],"genomes":[185],"few":[188],"other":[189],"collections":[190],"(including":[193],"human":[194],"microbiomes).":[195]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
