{"id":"https://openalex.org/W2142045367","doi":"https://doi.org/10.1093/nar/gkm1020","title":"InParanoid 6: eukaryotic ortholog clusters with inparalogs","display_name":"InParanoid 6: eukaryotic ortholog clusters with inparalogs","publication_year":2007,"publication_date":"2007-12-01","ids":{"openalex":"https://openalex.org/W2142045367","doi":"https://doi.org/10.1093/nar/gkm1020","mag":"2142045367","pmid":"https://pubmed.ncbi.nlm.nih.gov/18055500"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkm1020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm1020","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D263/7623993/gkm1020.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/36/suppl_1/D263/7623993/gkm1020.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112912070","display_name":"Anders Berglund","orcid":null},"institutions":[{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"A.-C. Berglund","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala, Sweden","institution_ids":["https://openalex.org/I223464139","https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031802675","display_name":"Erik Sj\u00f6lund","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"E. Sjolund","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088798683","display_name":"Gabriel \u00d6stlund","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"G. Ostlund","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032432650","display_name":"Erik L. L. Sonnhammer","orcid":"https://orcid.org/0000-0002-9015-5588"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I4210135511","display_name":"AlbaNova","ror":"https://ror.org/044kkfr75","country_code":"SE","type":"facility","lineage":["https://openalex.org/I4210135511"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"E. L. L. Sonnhammer","raw_affiliation_strings":["Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden","Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I4210135511","https://openalex.org/I161593684"]},{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2 Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I123387679"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5112912070"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I223464139","https://openalex.org/I2800139495"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":10.489,"has_fulltext":true,"cited_by_count":221,"citation_normalized_percentile":{"value":0.99021486,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"36","issue":"Database","first_page":"D263","last_page":"D266"},"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.935330867767334},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5460335612297058},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5269073843955994},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.49913811683654785},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4594493806362152},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4490519165992737},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.43794625997543335}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.935330867767334},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5460335612297058},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5269073843955994},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.49913811683654785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4594493806362152},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4490519165992737},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.43794625997543335}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkm1020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm1020","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D263/7623993/gkm1020.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:18055500","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18055500","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:pubmedcentral.nih.gov:2238924","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2238924","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkm1020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm1020","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D263/7623993/gkm1020.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":[{"id":"https://metadata.un.org/sdg/15","score":0.5099999904632568,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322509","display_name":"Kungliga Tekniska H\u00f6gskolan","ror":"https://ror.org/026vcq606"},{"id":"https://openalex.org/F4320325669","display_name":"Stockholms Universitet","ror":"https://ror.org/05f0yaq80"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142045367.pdf","grobid_xml":"https://content.openalex.org/works/W2142045367.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1689369637","https://openalex.org/W2010562878","https://openalex.org/W2096525273","https://openalex.org/W2114250447","https://openalex.org/W2137441463","https://openalex.org/W2137464714","https://openalex.org/W2143335572","https://openalex.org/W2155606054","https://openalex.org/W2159266221","https://openalex.org/W2167188257","https://openalex.org/W2168048337","https://openalex.org/W2170252811","https://openalex.org/W4245543257"],"related_works":["https://openalex.org/W4249269756","https://openalex.org/W1974658577","https://openalex.org/W2987420353","https://openalex.org/W1491897707","https://openalex.org/W2316833920","https://openalex.org/W4377098514","https://openalex.org/W4387564043","https://openalex.org/W2290118617","https://openalex.org/W1975345997","https://openalex.org/W2019197244"],"abstract_inverted_index":{"The":[0,53,111],"InParanoid":[1,40,62,93,123],"eukaryotic":[2,24],"ortholog":[3,31,49,124],"database":[4],"(http://InParanoid.sbc.su.se/)":[5],"has":[6,95,115],"been":[7,96,116],"updated":[8],"to":[9],"version":[10],"6":[11],"and":[12,26,29,106],"is":[13,99],"now":[14],"based":[15],"on":[16],"35":[17],"species.":[18,74],"We":[19],"collected":[20],"all":[21,34],"available":[22],"'complete'":[23],"proteomes":[25],"Escherichia":[27],"coli,":[28],"calculated":[30],"groups":[32,50],"for":[33,101,104,107,118],"595":[35],"species":[36,55,89],"pairs":[37],"using":[38],"the":[39,72,78,88,109,122],"program.":[41],"This":[42],"resulted":[43],"in":[44,51,59,77],"2":[45],"642":[46],"187":[47],"pairwise":[48],"total.":[52],"orthology-based":[54],"relations":[56],"are":[57],"presented":[58],"an":[60],"orthophylogram.":[61],"clusters":[63],"contain":[64],"one":[65],"or":[66],"more":[67],"orthologs":[68,76],"from":[69,84],"each":[70],"of":[71,121],"two":[73],"Multiple":[75],"same":[79],"species,":[80],"i.e.":[81],"inparalogs,":[82],"result":[83],"gene":[85],"duplications":[86],"after":[87],"divergence.":[90],"A":[91],"new":[92],"website":[94],"developed":[97],"which":[98],"optimized":[100],"speed":[102],"both":[103],"users":[105],"updating":[108],"system.":[110],"XML":[112],"output":[113],"format":[114],"improved":[117],"efficient":[119],"processing":[120],"clusters.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":20},{"year":2012,"cited_by_count":27}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}
