{"id":"https://openalex.org/W2147169455","doi":"https://doi.org/10.1093/bioinformatics/bth500","title":"Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination","display_name":"Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination","publication_year":2004,"publication_date":"2004-08-27","ids":{"openalex":"https://openalex.org/W2147169455","doi":"https://doi.org/10.1093/bioinformatics/bth500","mag":"2147169455","pmid":"https://pubmed.ncbi.nlm.nih.gov/15333462"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth500","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth500","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030634521","display_name":"Graham Etherington","orcid":"https://orcid.org/0000-0002-5003-1425"},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I3018370718","display_name":"Quadram Institute","ror":"https://ror.org/04td3ys19","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I3018370718","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Graham J. Etherington","raw_affiliation_strings":["Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK. Graham.Etherington@bbsrc.ac.uk","Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK. Graham.Etherington@bbsrc.ac.uk","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I3018370718"]},{"raw_affiliation_string":"Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK","institution_ids":["https://openalex.org/I2799300731"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076940698","display_name":"Jo Dicks","orcid":"https://orcid.org/0000-0003-1300-5233"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jo Dicks","raw_affiliation_strings":["Computational Biology Group, John Innes Centre Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Group, John Innes Centre Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK#TAB#","institution_ids":["https://openalex.org/I100288624","https://openalex.org/I2799300731"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040574485","display_name":"Ian N. Roberts","orcid":"https://orcid.org/0000-0003-2737-9148"},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian N. Roberts","raw_affiliation_strings":["Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK","institution_ids":["https://openalex.org/I2799300731"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.7663,"has_fulltext":false,"cited_by_count":121,"citation_normalized_percentile":{"value":0.83986014,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"21","issue":"3","first_page":"278","last_page":"281"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10976","display_name":"Viral gastroenteritis research and epidemiology","score":0.3361000120639801,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10976","display_name":"Viral gastroenteritis research and epidemiology","score":0.3361000120639801,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.11240000277757645,"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/T10943","display_name":"Escherichia coli research studies","score":0.06650000065565109,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"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/recombination","display_name":"Recombination","score":0.7920621037483215},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.724353015422821},{"id":"https://openalex.org/keywords/recombinant-dna","display_name":"Recombinant DNA","score":0.5728891491889954},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5532622933387756},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5041993856430054},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.49817657470703125},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4704878628253937},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4513661861419678},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4274205267429352},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.42692068219184875},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4235532581806183},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31949469447135925}],"concepts":[{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.7920621037483215},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.724353015422821},{"id":"https://openalex.org/C40767141","wikidata":"https://www.wikidata.org/wiki/Q285697","display_name":"Recombinant DNA","level":3,"score":0.5728891491889954},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5532622933387756},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5041993856430054},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49817657470703125},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4704878628253937},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4513661861419678},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4274205267429352},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.42692068219184875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4235532581806183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31949469447135925}],"mesh":[{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth500","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth500","pdf_url":null,"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:15333462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15333462","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":"Evaluation Study"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5899999737739563}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1972819041","https://openalex.org/W1990096140","https://openalex.org/W2017133314","https://openalex.org/W2029011467","https://openalex.org/W2042789248","https://openalex.org/W2055043387","https://openalex.org/W2070324371","https://openalex.org/W2099857122","https://openalex.org/W2103072823","https://openalex.org/W2106549255","https://openalex.org/W2106882534","https://openalex.org/W2121278300","https://openalex.org/W2144141060","https://openalex.org/W2149886005","https://openalex.org/W2162168100","https://openalex.org/W2163400707"],"related_works":["https://openalex.org/W2274607931","https://openalex.org/W3005983903","https://openalex.org/W4385690213","https://openalex.org/W4206192742","https://openalex.org/W2367910728","https://openalex.org/W2388596151","https://openalex.org/W2380955571","https://openalex.org/W2377147155","https://openalex.org/W2001833591","https://openalex.org/W2116114258"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recombination":[1],"can":[2],"be":[3],"a":[4,16,79,85,103],"prevailing":[5],"drive":[6],"in":[7,23,97],"shaping":[8],"genome":[9],"evolution.":[10],"RAT":[11,65],"(Recombination":[12],"Analysis":[13],"Tool)":[14],"is":[15,42,106],"Java-based":[17],"tool":[18],"for":[19],"investigating":[20],"recombination":[21],"events":[22],"any":[24,33],"number":[25],"of":[26,32,57,78,82,88,94],"aligned":[27],"sequences":[28,37],"(protein":[29],"or":[30],"DNA)":[31],"length":[34],"(short":[35],"viral":[36,69,95],"to":[38,52,68],"full":[39],"genomes).":[40],"It":[41],"an":[43],"uncomplicated":[44],"and":[45,48,84],"intuitive":[46],"application":[47],"allows":[49],"the":[50,55,76,90],"user":[51],"view":[53],"only":[54],"regions":[56],"sequence":[58],"alignments":[59],"they":[60],"are":[61],"interested":[62],"in.":[63],"RESULTS:":[64],"was":[66,73],"applied":[67],"sequences.":[70],"Its":[71],"utility":[72],"demonstrated":[74],"through":[75],"detection":[77],"known":[80],"recombinant":[81],"HIV":[83],"detailed":[86],"analysis":[87],"Noroviruses,":[89],"most":[91],"common":[92],"cause":[93],"gastroenteritis":[96],"humans.":[98],"AVAILABILITY:":[99],"RAT,":[100],"along":[101],"with":[102],"user's":[104],"guide,":[105],"freely":[107],"available":[108],"from":[109],"http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm.":[110]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":11}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
