{"id":"https://openalex.org/W2011484562","doi":"https://doi.org/10.1016/s1672-0229(07)60014-x","title":"Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics","display_name":"Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics","publication_year":2007,"publication_date":"2007-03-01","ids":{"openalex":"https://openalex.org/W2011484562","doi":"https://doi.org/10.1016/s1672-0229(07)60014-x","mag":"2011484562","pmid":"https://pubmed.ncbi.nlm.nih.gov/17572364"},"language":"en","primary_location":{"id":"doi:10.1016/s1672-0229(07)60014-x","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(07)60014-x","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/s1672-0229(07)60014-x","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001456642","display_name":"Satoshi Tamaki","orcid":"https://orcid.org/0000-0001-9099-1036"},"institutions":[{"id":"https://openalex.org/I4210141715","display_name":"Keio University Shonan Fujisawa","ror":"https://ror.org/047khpn70","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210141715"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Tamaki","raw_affiliation_strings":["Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]},{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069148446","display_name":"Kazuharu Arakawa","orcid":"https://orcid.org/0000-0002-2893-4919"},"institutions":[{"id":"https://openalex.org/I4210141715","display_name":"Keio University Shonan Fujisawa","ror":"https://ror.org/047khpn70","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210141715"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kazuharu Arakawa","raw_affiliation_strings":["Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014166632","display_name":"Nobuaki Kono","orcid":"https://orcid.org/0000-0001-5960-7956"},"institutions":[{"id":"https://openalex.org/I4210141715","display_name":"Keio University Shonan Fujisawa","ror":"https://ror.org/047khpn70","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210141715"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Nobuaki Kono","raw_affiliation_strings":["Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]},{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015575713","display_name":"Masaru Tomita","orcid":"https://orcid.org/0000-0003-3423-377X"},"institutions":[{"id":"https://openalex.org/I4210141715","display_name":"Keio University Shonan Fujisawa","ror":"https://ror.org/047khpn70","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210141715"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaru Tomita","raw_affiliation_strings":["Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan"],"affiliations":[{"raw_affiliation_string":"Department of Environmental Information, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]},{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University , Fujisawa, 252-8520 , Japan","institution_ids":["https://openalex.org/I4210141715"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5069148446"],"corresponding_institution_ids":["https://openalex.org/I4210141715"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.5378,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65014015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","issue":"1","first_page":"53","last_page":"58"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9929999709129333,"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"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9923999905586243,"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/annotation","display_name":"Annotation","score":0.8883882761001587},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7218575477600098},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.6405890583992004},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5349648594856262},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5312153100967407},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5108373165130615},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.43870794773101807},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.43692469596862793},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.436271607875824},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3457754850387573},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26995912194252014},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15161100029945374}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8883882761001587},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7218575477600098},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.6405890583992004},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5349648594856262},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5312153100967407},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5108373165130615},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.43870794773101807},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.43692469596862793},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.436271607875824},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3457754850387573},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26995912194252014},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15161100029945374}],"mesh":[{"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/s1672-0229(07)60014-x","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(07)60014-x","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17572364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17572364","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4016466","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054091","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/s1672-0229(07)60014-x","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(07)60014-x","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.5099999904632568,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G5256887504","display_name":null,"funder_award_id":"Japan Society for the Promotion of Science (JSPS)","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7752643416","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320909","display_name":"Keio University","ror":"https://ror.org/02kn6nx58"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W202652404","https://openalex.org/W1839423960","https://openalex.org/W1885254586","https://openalex.org/W1944107535","https://openalex.org/W1972744519","https://openalex.org/W1975796937","https://openalex.org/W1978294135","https://openalex.org/W2011261850","https://openalex.org/W2041652393","https://openalex.org/W2055043387","https://openalex.org/W2057099031","https://openalex.org/W2082351454","https://openalex.org/W2088607230","https://openalex.org/W2093080343","https://openalex.org/W2100882223","https://openalex.org/W2103017472","https://openalex.org/W2107903949","https://openalex.org/W2110041134","https://openalex.org/W2110400517","https://openalex.org/W2113601822","https://openalex.org/W2121764497","https://openalex.org/W2124931735","https://openalex.org/W2133253129","https://openalex.org/W2133787379","https://openalex.org/W2134153749","https://openalex.org/W2136145671","https://openalex.org/W2141885858","https://openalex.org/W2148004368","https://openalex.org/W2150934173","https://openalex.org/W2151831732","https://openalex.org/W2154202919","https://openalex.org/W2155606054","https://openalex.org/W2160375677","https://openalex.org/W2160764161","https://openalex.org/W2161062388","https://openalex.org/W2164926676","https://openalex.org/W4210241463","https://openalex.org/W4210400672","https://openalex.org/W4211083314","https://openalex.org/W4245145908","https://openalex.org/W4293196852","https://openalex.org/W6608181635","https://openalex.org/W6638940392","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2901823680","https://openalex.org/W2946410450","https://openalex.org/W2059565715","https://openalex.org/W1999129612","https://openalex.org/W2162782320","https://openalex.org/W2009940763","https://openalex.org/W3111061871","https://openalex.org/W1760213857","https://openalex.org/W110079389","https://openalex.org/W2099626126"],"abstract_inverted_index":{"Annotations":[0],"of":[1,14,31,35,107],"complete":[2,36],"genome":[3,44,52,64],"sequences":[4],"submitted":[5],"directly":[6],"from":[7],"sequencing":[8],"projects":[9],"are":[10,41],"diverse":[11],"in":[12,99,113],"terms":[13],"annotation":[15,106],"strategies":[16],"and":[17,39,86,122],"update":[18],"frequencies.":[19],"These":[20],"inconsistencies":[21],"make":[22],"comparative":[23],"studies":[24],"difficult.":[25],"To":[26],"allow":[27],"rapid":[28,51],"data":[29],"preparation":[30],"a":[32,63],"large":[33],"number":[34],"genomes,":[37],"automation":[38],"speed":[40],"important":[42],"for":[43,58,95],"re-annotation.":[45],"Here":[46],"we":[47],"introduce":[48],"an":[49],"open-source":[50],"re-annotation":[53],"software":[54],"system,":[55],"Restauro-G,":[56],"specialized":[57],"bacterial":[59,97],"genomes.":[60],"Restauro-G":[61,90,110],"re-annotates":[62],"by":[65,89],"similarity":[66],"searches":[67],"utilizing":[68],"the":[69,102,114,127],"BLAST-Like":[70],"Alignment":[71],"Tool,":[72],"referring":[73],"to":[74],"protein":[75],"databases":[76],"such":[77],"as":[78],"UniProt":[79],"KB,":[80],"NCBI":[81,83],"nr,":[82],"COGs,":[84],"Pfam,":[85],"PSORTb.":[87],"Re-annotation":[88],"achieved":[91],"over":[92],"98%":[93],"accuracy":[94],"most":[96],"chromosomes":[98],"comparison":[100],"with":[101],"original":[103],"manually":[104],"curated":[105],"EMBL":[108],"releases.":[109],"was":[111],"developed":[112],"generic":[115],"bioinformatics":[116],"workbench":[117],"G-language":[118],"Genome":[119],"Analysis":[120],"Environment":[121],"is":[123],"distributed":[124],"at":[125],"http://restauro-g.iab.keio.ac.jp/under":[126],"GNU":[128],"General":[129],"Public":[130],"License.":[131]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}