{"id":"https://openalex.org/W1976363628","doi":"https://doi.org/10.1093/nar/gkp329","title":"d-Omix: a mixer of generic protein domain analysis tools","display_name":"d-Omix: a mixer of generic protein domain analysis tools","publication_year":2009,"publication_date":"2009-05-21","ids":{"openalex":"https://openalex.org/W1976363628","doi":"https://doi.org/10.1093/nar/gkp329","mag":"1976363628","pmid":"https://pubmed.ncbi.nlm.nih.gov/19465389"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkp329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp329","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W417/3927407/gkp329.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/37/suppl_2/W417/3927407/gkp329.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035554261","display_name":"Duangdao Wichadakul","orcid":"https://orcid.org/0000-0002-8802-2524"},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":true,"raw_author_name":"D. Wichadakul","raw_affiliation_strings":["National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory, Pathumthani, Thailand. duangdao.wic@biotec.or.th","National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory, Pathumthani, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory, Pathumthani, Thailand. duangdao.wic@biotec.or.th","institution_ids":["https://openalex.org/I902798049"]},{"raw_affiliation_string":"National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory, Pathumthani, Thailand","institution_ids":["https://openalex.org/I902798049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086527435","display_name":"Somrak Numnark","orcid":null},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"S. Numnark","raw_affiliation_strings":["National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory (ISL), Pathumthani, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory (ISL), Pathumthani, Thailand","institution_ids":["https://openalex.org/I902798049"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090289533","display_name":"Supawadee Ingsriswang","orcid":"https://orcid.org/0000-0002-3183-5997"},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"S. Ingsriswang","raw_affiliation_strings":["National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory (ISL), Pathumthani, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genetic Engineering and Biotechnology (BIOTEC) - Information Systems Laboratory (ISL), Pathumthani, Thailand","institution_ids":["https://openalex.org/I902798049"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5035554261"],"corresponding_institution_ids":["https://openalex.org/I902798049"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.135,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.52512912,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"37","issue":"Web Server","first_page":"W417","last_page":"W421"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9968000054359436,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9940999746322632,"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/domain","display_name":"Domain (mathematical analysis)","score":0.6644108295440674},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6365876197814941},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.6093109846115112},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5527382493019104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5472828149795532},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5291481614112854},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.47710567712783813},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4495672583580017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42527350783348083},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36813944578170776},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.24854594469070435},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19229406118392944},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19193917512893677},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13941580057144165}],"concepts":[{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6644108295440674},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6365876197814941},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.6093109846115112},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5527382493019104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5472828149795532},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5291481614112854},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.47710567712783813},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4495672583580017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42527350783348083},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36813944578170776},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.24854594469070435},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19229406118392944},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19193917512893677},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13941580057144165},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D011506","descriptor_name":"Proteins","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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkp329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp329","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W417/3927407/gkp329.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:19465389","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19465389","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:2703976","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2703976","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/gkp329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp329","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W417/3927407/gkp329.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":[],"funders":[{"id":"https://openalex.org/F4320322437","display_name":"National Science and Technology Development Agency","ror":"https://ror.org/04vy95b61"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1976363628.pdf","grobid_xml":"https://content.openalex.org/works/W1976363628.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1768635289","https://openalex.org/W1971155547","https://openalex.org/W1986512768","https://openalex.org/W1989509003","https://openalex.org/W2001914359","https://openalex.org/W2012481064","https://openalex.org/W2019739870","https://openalex.org/W2045839655","https://openalex.org/W2063252182","https://openalex.org/W2085277871","https://openalex.org/W2091448229","https://openalex.org/W2098354205","https://openalex.org/W2098791869","https://openalex.org/W2104265053","https://openalex.org/W2106882534","https://openalex.org/W2108067237","https://openalex.org/W2109715166","https://openalex.org/W2112090702","https://openalex.org/W2112792893","https://openalex.org/W2118340207","https://openalex.org/W2122576958","https://openalex.org/W2126411786","https://openalex.org/W2133070552","https://openalex.org/W2136975468","https://openalex.org/W2141293686","https://openalex.org/W2142008033","https://openalex.org/W2144494426","https://openalex.org/W2145427519","https://openalex.org/W2146312020","https://openalex.org/W2157346087","https://openalex.org/W2161033884","https://openalex.org/W2161394740","https://openalex.org/W2168549338","https://openalex.org/W2169397265","https://openalex.org/W3199943451","https://openalex.org/W3216627664","https://openalex.org/W4256395558"],"related_works":["https://openalex.org/W2362218761","https://openalex.org/W2062354928","https://openalex.org/W2113708670","https://openalex.org/W2088120817","https://openalex.org/W3116784128","https://openalex.org/W3165639034","https://openalex.org/W2137974866","https://openalex.org/W4252097797","https://openalex.org/W2138458178","https://openalex.org/W2149044412"],"abstract_inverted_index":{"Domain":[0,28],"combination":[1],"provides":[2],"important":[3],"clues":[4],"to":[5,36],"the":[6,62,88,99,114,159,192],"roles":[7],"of":[8,26,47,57,104,116,140],"protein":[9,12,41,48,55,73,83,105,127,180],"domains":[10,106],"in":[11,44],"function,":[13],"interaction":[14],"and":[15,39,97,102,144,165,175],"evolution.":[16],"We":[17],"have":[18],"developed":[19],"a":[20,33,78,91,108,125,138,154,188],"web":[21,198],"server":[22,63,193,199],"d-Omix":[23,160,197],"(a":[24],"Mixer":[25],"Protein":[27],"Analysis":[29],"Tools)":[30],"aiming":[31],"as":[32,171,194],"unified":[34],"platform":[35],"analyze,":[37],"compare":[38],"visualize":[40],"data":[42,142],"sets":[43,56],"various":[45,168],"aspects":[46],"domain":[49,68,84,109,147],"combinations.":[50],"With":[51],"InterProScan":[52,185],"files":[53,143],"for":[54,67,153],"interest":[58],"provided":[59,190],"by":[60,191],"users,":[61],"incorporates":[64],"four":[65],"services":[66],"analyses.":[69],"First,":[70],"it":[71,95,112,123],"constructs":[72],"phylogenetic":[74],"tree":[75],"based":[76,118],"on":[77,119],"distance":[79],"matrix":[80],"calculated":[81],"from":[82,130,133,158],"architectures":[85],"(DAs),":[86],"allowing":[87],"comparison":[89],"with":[90,178],"sequence-based":[92],"tree.":[93],"Second,":[94],"calculates":[96],"visualizes":[98],"versatility,":[100],"abundance":[101],"co-presence":[103],"via":[107],"graph.":[110],"Third,":[111],"compares":[113],"similarity":[115],"proteins":[117],"DA":[120],"alignment.":[121],"Fourth,":[122],"builds":[124],"putative":[126],"network":[128],"derived":[129],"domain-domain":[131],"interactions":[132],"DOMINE.":[134],"Users":[135,177],"may":[136],"select":[137],"variety":[139],"input":[141],"flexibly":[145],"choose":[146],"search":[148],"tools":[149],"(e.g.":[150],"hmmpfam,":[151],"superfamily)":[152],"specific":[155],"analysis.":[156],"Results":[157],"could":[161,182],"be":[162],"interactively":[163],"explored":[164],"exported":[166],"into":[167],"formats":[169],"such":[170],"SVG,":[172],"JPG,":[173],"BMP":[174],"CSV.":[176],"only":[179],"sequences":[181],"prepare":[183],"an":[184],"file":[186],"using":[187],"service":[189],"well.":[195],"The":[196],"is":[200],"freely":[201],"available":[202],"at":[203],"http://www.biotec.or.th/isl/Domix.":[204]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
