{"id":"https://openalex.org/W2109750550","doi":"https://doi.org/10.1093/bioinformatics/btt582","title":"orthAgogue: an agile tool for the rapid prediction of orthology relations","display_name":"orthAgogue: an agile tool for the rapid prediction of orthology relations","publication_year":2013,"publication_date":"2013-10-09","ids":{"openalex":"https://openalex.org/W2109750550","doi":"https://doi.org/10.1093/bioinformatics/btt582","mag":"2109750550","pmid":"https://pubmed.ncbi.nlm.nih.gov/24115168"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt582","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt582","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/A5089900166","display_name":"Ole Kristian Ekseth","orcid":null},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ole Kristian Ekseth","raw_affiliation_strings":["Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077915624","display_name":"Martin Kuiper","orcid":"https://orcid.org/0000-0002-1171-9876"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Martin Kuiper","raw_affiliation_strings":["Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080056836","display_name":"Vladimir Mironov","orcid":"https://orcid.org/0000-0002-9454-5823"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Vladimir Mironov","raw_affiliation_strings":["Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089900166"],"corresponding_institution_ids":["https://openalex.org/I204778367"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.5733,"has_fulltext":false,"cited_by_count":119,"citation_normalized_percentile":{"value":0.93785991,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"30","issue":"5","first_page":"734","last_page":"736"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7615000009536743,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7615000009536743,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.06400000303983688,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.04230000078678131,"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/agile-software-development","display_name":"Agile software development","score":0.758960485458374},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7522486448287964},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5719587802886963},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5405222177505493},{"id":"https://openalex.org/keywords/source-lines-of-code","display_name":"Source lines of code","score":0.4806472361087799},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.45554935932159424},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4291476011276245},{"id":"https://openalex.org/keywords/software-quality","display_name":"Software quality","score":0.4257199466228485},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32900065183639526},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3171108365058899},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.22098928689956665}],"concepts":[{"id":"https://openalex.org/C14185376","wikidata":"https://www.wikidata.org/wiki/Q30232","display_name":"Agile software development","level":2,"score":0.758960485458374},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7522486448287964},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5719587802886963},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5405222177505493},{"id":"https://openalex.org/C199519371","wikidata":"https://www.wikidata.org/wiki/Q942695","display_name":"Source lines of code","level":3,"score":0.4806472361087799},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45554935932159424},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4291476011276245},{"id":"https://openalex.org/C117447612","wikidata":"https://www.wikidata.org/wiki/Q1412670","display_name":"Software quality","level":4,"score":0.4257199466228485},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32900065183639526},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3171108365058899},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.22098928689956665}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt582","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt582","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:24115168","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24115168","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":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1552559843","https://openalex.org/W1902354325","https://openalex.org/W1977027195","https://openalex.org/W2008856488","https://openalex.org/W2037883697","https://openalex.org/W2048448217","https://openalex.org/W2055043387","https://openalex.org/W2124166542","https://openalex.org/W2133790733","https://openalex.org/W2154364831","https://openalex.org/W2155606054","https://openalex.org/W2167188257","https://openalex.org/W2288176647","https://openalex.org/W3210308821","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1992074508","https://openalex.org/W4380568682","https://openalex.org/W2033235985","https://openalex.org/W2086523506","https://openalex.org/W2763289028","https://openalex.org/W2031796104","https://openalex.org/W4361792201","https://openalex.org/W4308641625","https://openalex.org/W2953504043","https://openalex.org/W3141545746"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,67,76],"comparison":[2],"of":[3,52],"genes":[4],"and":[5,32,62,79],"gene":[6,19],"products":[7],"across":[8],"species":[9],"depends":[10],"on":[11],"high-quality":[12],"tools":[13],"to":[14],"determine":[15],"the":[16,73],"relationships":[17],"between":[18],"or":[20],"protein":[21],"sequences":[22],"from":[23],"various":[24],"species.":[25],"Although":[26],"some":[27],"excellent":[28],"applications":[29],"are":[30,84],"available":[31,85],"widely":[33],"used,":[34],"their":[35],"performance":[36],"leaves":[37],"room":[38],"for":[39,49,82],"improvement.":[40],"RESULTS:":[41],"We":[42],"developed":[43],"orthAgogue:":[44],"a":[45,60],"multithreaded":[46],"C":[47],"application":[48],"high-speed":[50],"estimation":[51],"homology":[53],"relations":[54],"in":[55],"massive":[56],"datasets,":[57],"operated":[58],"via":[59],"flexible":[61],"easy":[63],"command-line":[64],"interface.":[65],"AVAILABILITY:":[66],"orthAgogue":[68],"software":[69],"is":[70],"distributed":[71],"under":[72],"GNU":[74],"license.":[75],"source":[77],"code":[78],"binaries":[80],"compiled":[81],"Linux":[83],"at":[86],"https://code.google.com/p/orthagogue/.":[87]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-12T21:12:35.861297","created_date":"2025-10-10T00:00:00"}
