{"id":"https://openalex.org/W2142000458","doi":"https://doi.org/10.1186/1471-2105-7-472","title":"CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes","display_name":"CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes","publication_year":2006,"publication_date":"2006-10-24","ids":{"openalex":"https://openalex.org/W2142000458","doi":"https://doi.org/10.1186/1471-2105-7-472","mag":"2142000458","pmid":"https://pubmed.ncbi.nlm.nih.gov/17062155","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/1643837"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-472","doi":"https://doi.org/10.1186/1471-2105-7-472","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-472","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-472","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-472","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009003438","display_name":"Ikuo Uchiyama","orcid":"https://orcid.org/0000-0002-9197-5000","observed_orcids":["https://orcid.org/0000-0002-9197-5000"]},"institutions":[{"id":"https://openalex.org/I138804964","display_name":"National Institute for Basic Biology","ror":"https://ror.org/05q8wtt20","country_code":"JP","type":"education","lineage":["https://openalex.org/I1319490839","https://openalex.org/I138804964","https://openalex.org/I199525922"]},{"id":"https://openalex.org/I199525922","display_name":"National Institutes of Natural Sciences","ror":"https://ror.org/055n47h92","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I199525922"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ikuo Uchiyama","raw_affiliation_strings":["National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan. uchiyama@nibb.ac.jp","National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan. uchiyama@nibb.ac.jp","institution_ids":["https://openalex.org/I138804964","https://openalex.org/I199525922"]},{"raw_affiliation_string":"National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan","institution_ids":["https://openalex.org/I138804964","https://openalex.org/I199525922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113107559","display_name":"Toshio Higuchi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405275523","display_name":"Intec WEB And Genome Informatics Corporation (Japan)","ror":"https://ror.org/03rd22b31","country_code":"JP","type":"company","lineage":["https://openalex.org/I4405275523"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshio Higuchi","raw_affiliation_strings":["INTEC Web and Genome Informatics Corporation, 1-3-3 Shinsuna, Koto-ku, Tokyo, 136-0075, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INTEC Web and Genome Informatics Corporation, 1-3-3 Shinsuna, Koto-ku, Tokyo, 136-0075, Japan","institution_ids":["https://openalex.org/I4405275523"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022775273","display_name":"Ichizo Kobayashi","orcid":"https://orcid.org/0000-0002-3854-1879","observed_orcids":["https://orcid.org/0000-0002-3854-1879"]},"institutions":[{"id":"https://openalex.org/I4405286826","display_name":"Institute of Medical Science, The University of Tokyo","ror":"https://ror.org/0376e0j29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4405286826","https://openalex.org/I74801974"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ichizo Kobayashi","raw_affiliation_strings":["Department of Medical Genome Sciences, Graduate School of Frontier Science & Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan","Graduate Program of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Genome Sciences, Graduate School of Frontier Science & Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I4405286826","https://openalex.org/I74801974"]},{"raw_affiliation_string":"Graduate Program of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009003438"],"corresponding_institution_ids":["https://openalex.org/I138804964","https://openalex.org/I199525922"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.3469,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.76053204,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"7","issue":"1","first_page":"472","last_page":"472"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9945999979972839,"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":0.9945999979972839,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.004800000227987766,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":9.999999747378752e-05,"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/comparative-genomics","display_name":"comparative genomics","score":0.9459999799728394},{"id":"https://openalex.org/keywords/closely-related-genomes","display_name":"closely related genomes","score":0.6909999847412109},{"id":"https://openalex.org/keywords/genomic-rearrangements","display_name":"genome rearrangement","score":0.6309999823570251},{"id":"https://openalex.org/keywords/indels","display_name":"indels","score":0.8510000109672546},{"id":"https://openalex.org/keywords/inversion","display_name":"inversion","score":0.8069999814033508},{"id":"https://openalex.org/keywords/translocation","display_name":"translocation","score":0.9649999737739563},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"gene duplication","score":0.7760000228881836},{"id":"https://openalex.org/keywords/ortholog-identification","display_name":"ortholog identification","score":0.8059999942779541},{"id":"https://openalex.org/keywords/tandem-repeats","display_name":"tandem repeats","score":0.7549999952316284},{"id":"https://openalex.org/keywords/repetitive-dna","display_name":"repetitive DNA","score":0.6380000114440918},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC content","score":0.7590000033378601},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"codon usage bias","score":0.9990000128746033},{"id":"https://openalex.org/keywords/bacterial-evolution","display_name":"bacterial evolution","score":0.46799999475479126},{"id":"https://openalex.org/keywords/archaeal-evolution","display_name":"archaeal evolution","score":0.875}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7232834696769714},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5806615948677063},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5526156425476074},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.528926432132721},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5015056133270264},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4959324300289154},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.49131813645362854},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.47135892510414124},{"id":"https://openalex.org/C59046462","wikidata":"https://www.wikidata.org/wiki/Q181319","display_name":"Scrolling","level":2,"score":0.4700091481208801},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.43278759717941284},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4265033006668091},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4187612235546112},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4102970361709595},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4024650454521179},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29238906502723694},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25658196210861206},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17893418669700623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","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":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","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":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019779","descriptor_name":"Salmonella enterica","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-7-472","doi":"https://doi.org/10.1186/1471-2105-7-472","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-472","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-472","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17062155","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17062155","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,"listed_in":[],"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":"BMC bioinformatics","raw_type":"Comparative Study"},{"id":"pmh:oai:pubmedcentral.nih.gov:1643837","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC1643837/","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,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:6ecb176d1450475089ac4c80acbea747","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/6ecb176d1450475089ac4c80acbea747","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 472 (2006)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-472","doi":"https://doi.org/10.1186/1471-2105-7-472","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-472","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-472","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2560689047","display_name":"Role of selfish restriction-modification gene complexes in genome evolution : comparative genomics and experimental evolution","funder_award_id":"15370099","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2998738995","display_name":"Death and regeneration of genome Biology of DNAdouble-strand break and the response","funder_award_id":"13141201","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6973133816","display_name":"Selfish genetic elements involved both in the maintenance and rearrangement of the genome","funder_award_id":"17310113","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142000458.pdf","grobid_xml":"https://content.openalex.org/works/W2142000458.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1133173477","https://openalex.org/W1482360569","https://openalex.org/W1594542446","https://openalex.org/W1935763178","https://openalex.org/W1964918240","https://openalex.org/W1968146772","https://openalex.org/W1993023516","https://openalex.org/W2011820950","https://openalex.org/W2015292449","https://openalex.org/W2016299826","https://openalex.org/W2027448315","https://openalex.org/W2030205072","https://openalex.org/W2032610035","https://openalex.org/W2034869114","https://openalex.org/W2035581898","https://openalex.org/W2035634951","https://openalex.org/W2038605324","https://openalex.org/W2055666215","https://openalex.org/W2055771302","https://openalex.org/W2068787541","https://openalex.org/W2074231493","https://openalex.org/W2075882880","https://openalex.org/W2077365137","https://openalex.org/W2089431713","https://openalex.org/W2095685450","https://openalex.org/W2099836442","https://openalex.org/W2100882223","https://openalex.org/W2101719812","https://openalex.org/W2110132014","https://openalex.org/W2110291136","https://openalex.org/W2120713200","https://openalex.org/W2121024740","https://openalex.org/W2123546399","https://openalex.org/W2128591967","https://openalex.org/W2133253129","https://openalex.org/W2134153749","https://openalex.org/W2135146244","https://openalex.org/W2136145671","https://openalex.org/W2137158472","https://openalex.org/W2139243714","https://openalex.org/W2140029549","https://openalex.org/W2142619120","https://openalex.org/W2144866873","https://openalex.org/W2146180248","https://openalex.org/W2149452073","https://openalex.org/W2152331922","https://openalex.org/W2155237411","https://openalex.org/W2156273926","https://openalex.org/W2158714788","https://openalex.org/W2161387979","https://openalex.org/W2162423297","https://openalex.org/W2165627817","https://openalex.org/W2610179052","https://openalex.org/W7097764011","https://openalex.org/W7098915344"],"related_works":["https://openalex.org/W4396688623","https://openalex.org/W4388223022","https://openalex.org/W1133173477","https://openalex.org/W7097779675","https://openalex.org/W2139063835","https://openalex.org/W2085814327","https://openalex.org/W3134090705","https://openalex.org/W2516918425","https://openalex.org/W1984369653","https://openalex.org/W1594542446"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"recent":[2],"accumulation":[3],"of":[4,16,20,38,70,116,125,145,240,257,263,278],"closely":[5,71,284,301],"related":[6,72,285,302],"genomic":[7,40,148,298],"sequences":[8,131],"provides":[9,233],"a":[10,59,234,292],"valuable":[11],"resource":[12],"for":[13,171,208,212,221,237,295],"the":[14,17,36,107,123,143,146,156,161,173,188,218,238,255,275],"elucidation":[15],"evolutionary":[18,276],"histories":[19],"various":[21,202,244],"organisms.":[22],"However,":[23],"although":[24],"numerous":[25],"alignment":[26,94,174,189,196,214,248,259,306],"calculation":[27,239],"and":[28,49,93,98,101,132,182,210,228,287,308],"visualization":[29],"tools":[30,312],"have":[31,57,266],"been":[32,267],"developed":[33,58],"to":[34,80,104,152,253,273],"date,":[35],"analysis":[37,62,311],"complex":[39,280,297],"changes,":[41],"such":[42,121,216],"as":[43,122,176,217,247],"large":[44],"insertions,":[45],"deletions,":[46],"inversions,":[47],"translocations":[48],"duplications,":[50],"still":[51],"presents":[52],"certain":[53],"difficulties.":[54],"RESULTS:":[55],"We":[56],"comparative":[60],"genome":[61,88,281],"tool,":[63],"named":[64],"CGAT,":[65],"which":[66,200,250],"allows":[67,102,251],"detailed":[68],"comparisons":[69],"bacteria-sized":[73],"genomes":[74,303],"mainly":[75],"through":[76],"visualizing":[77],"middle-to-large-scale":[78],"changes":[79,133,282,299],"infer":[81,274],"underlying":[82],"mechanisms.":[83],"CGAT":[84,192,232,290],"displays":[85],"precomputed":[86,154],"pairwise":[87],"alignments":[89,162,242],"on":[90,118],"both":[91],"dotplot":[92],"viewers":[95],"with":[96,314],"scrolling":[97],"zooming":[99],"functions,":[100],"users":[103,252],"move":[105],"along":[106],"pre-identified":[108],"orthologous":[109],"alignments.":[110],"Users":[111],"can":[112,158,183],"place":[113],"several":[114],"types":[115],"information":[117],"this":[119,166,264],"alignment,":[120],"presence":[124],"tandem":[126],"repeats":[127],"or":[128,137],"interspersed":[129],"repetitive":[130],"in":[134,270],"G+C":[135],"contents":[136],"codon":[138],"usage":[139],"bias,":[140],"thereby":[141],"facilitating":[142],"interpretation":[144],"observed":[147],"changes.":[149],"In":[150],"addition":[151],"displaying":[153],"alignments,":[155,224,227],"viewer":[157],"dynamically":[159],"calculate":[160],"between":[163,185,283,300],"specified":[164],"regions;":[165],"feature":[167],"is":[168,291],"especially":[169],"useful":[170],"examining":[172],"boundaries,":[175],"these":[177],"boundaries":[178],"are":[179,205],"often":[180],"obscure":[181],"vary":[184],"programs.":[186,260],"Besides":[187],"browser":[190],"functionalities,":[191],"also":[193],"contains":[194,201],"an":[195],"data":[197],"construction":[198],"module,":[199],"procedures":[203],"that":[204],"commonly":[206],"used":[207,268],"pre-":[209],"post-processing":[211],"large-scale":[213],"calculation,":[215],"split-and-merge":[219],"protocol":[220],"calculating":[222],"long":[223],"chaining":[225],"adjacent":[226],"ortholog":[229],"identification.":[230],"Indeed,":[231],"general":[235],"framework":[236],"genome-scale":[241],"using":[243,304],"existing":[245,305],"programs":[246,307],"engines,":[249],"compare":[254],"outputs":[256],"different":[258],"Earlier":[261],"versions":[262],"program":[265],"successfully":[269],"our":[271],"research":[272],"history":[277],"apparently":[279],"eubacteria":[286],"archaea.":[288],"CONCLUSION:":[289],"practical":[293],"tool":[294],"analyzing":[296],"other":[309],"sequence":[310],"combined":[313],"extensive":[315],"manual":[316],"inspection.":[317]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}