{"id":"https://openalex.org/W2149292785","doi":"https://doi.org/10.1093/bioinformatics/btp078","title":"A web-based software system for dynamic gene cluster comparison across multiple genomes","display_name":"A web-based software system for dynamic gene cluster comparison across multiple genomes","publication_year":2009,"publication_date":"2009-02-09","ids":{"openalex":"https://openalex.org/W2149292785","doi":"https://doi.org/10.1093/bioinformatics/btp078","mag":"2149292785","pmid":"https://pubmed.ncbi.nlm.nih.gov/19208612"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp078","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/956/48984257/bioinformatics_25_7_956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/956/48984257/bioinformatics_25_7_956.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061160395","display_name":"Kashi V. Revanna","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kashi Vishwanath Revanna","raw_affiliation_strings":["Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069527016","display_name":"Vivek Krishnakumar","orcid":"https://orcid.org/0000-0002-5227-0200"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vivek Krishnakumar","raw_affiliation_strings":["Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088669922","display_name":"Qunfeng Dong","orcid":"https://orcid.org/0000-0002-4610-1670"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qunfeng Dong","raw_affiliation_strings":["Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088669922"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1369,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.56301506,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"25","issue":"7","first_page":"956","last_page":"957"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6765999794006348,"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":0.6765999794006348,"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":0.23510000109672546,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02800000086426735,"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/genome","display_name":"Genome","score":0.7718145847320557},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6620256900787354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6351830959320068},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5931071639060974},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.5096640586853027},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.4998157024383545},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.48601585626602173},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4556248188018799},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39891695976257324},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37606579065322876},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34097468852996826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28278422355651855},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22690489888191223},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2254246175289154}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7718145847320557},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6620256900787354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6351830959320068},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5931071639060974},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5096640586853027},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.4998157024383545},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.48601585626602173},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4556248188018799},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39891695976257324},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37606579065322876},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34097468852996826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28278422355651855},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22690489888191223},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2254246175289154},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp078","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/956/48984257/bioinformatics_25_7_956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19208612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19208612","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp078","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/956/48984257/bioinformatics_25_7_956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6800000071525574,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307758","display_name":"Eli Lilly and Company","ror":"https://ror.org/01qat3289"},{"id":"https://openalex.org/F4320309409","display_name":"Lilly Endowment","ror":"https://ror.org/00cpsd622"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149292785.pdf","grobid_xml":"https://content.openalex.org/works/W2149292785.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1263422348","https://openalex.org/W1965178844","https://openalex.org/W1984345785","https://openalex.org/W2007447692","https://openalex.org/W2019386061","https://openalex.org/W2044741718","https://openalex.org/W2090385974","https://openalex.org/W2142000458","https://openalex.org/W2158714788","https://openalex.org/W2167734008","https://openalex.org/W2169267759","https://openalex.org/W4210430020","https://openalex.org/W4240231372","https://openalex.org/W4248664566","https://openalex.org/W6628043643"],"related_works":["https://openalex.org/W189065216","https://openalex.org/W2521866209","https://openalex.org/W1965280193","https://openalex.org/W3177323319","https://openalex.org/W3023271652","https://openalex.org/W2141886348","https://openalex.org/W1641614871","https://openalex.org/W2123222904","https://openalex.org/W2978947208","https://openalex.org/W2093610003"],"abstract_inverted_index":{"SUMMARY:":[0],"Investigating":[1],"the":[2,16,45,88,96,117],"conservation":[3,99],"of":[4,18,62,82,90,124],"gene":[5,97],"clusters":[6],"across":[7],"multiple":[8],"genomes":[9,89,144],"has":[10],"become":[11],"a":[12,59,71,80,101],"standard":[13],"practice":[14],"in":[15,58],"era":[17],"comparative":[19],"genomics.":[20],"However,":[21],"all":[22],"existing":[23],"software":[24,73,151],"and":[25,43,93,111,142],"databases":[26],"rely":[27],"heavily":[28],"on":[29],"pre-computation":[30],"to":[31,65,78,114,120,139,145],"identify":[32],"homologous":[33],"genes":[34,123],"by":[35],"genome-wide":[36,109],"comparisons.":[37],"Such":[38],"pre-computing":[39,110],"strategies":[40],"lack":[41],"accuracy":[42],"updating":[44],"data":[46],"is":[47,152],"computationally":[48],"intensive.":[49],"Since":[50],"most":[51],"molecular":[52],"biologists":[53],"are":[54],"often":[55],"interested":[56],"only":[57],"small":[60],"cluster":[61,98],"genes,":[63,83],"catering":[64],"this":[66],"need,":[67],"we":[68],"have":[69,136],"developed":[70],"web-based":[72],"system":[74,127],"that":[75],"allows":[76,112],"users":[77,113],"upload":[79],"list":[81],"perform":[84],"dynamic":[85],"search":[86,118],"against":[87],"their":[91,122],"choices":[92],"interactively":[94],"visualize":[95],"using":[100],"novel":[102],"multi-genome":[103],"browser.":[104],"Our":[105,126,150],"approach":[106],"avoids":[107],"expensive":[108],"dynamically":[115],"change":[116],"criteria":[119],"fit":[121],"interest.":[125],"can":[128],"be":[129],"customized":[130],"for":[131],"any":[132],"genome":[133],"sequences.":[134],"We":[135],"applied":[137],"it":[138],"both":[140],"prokaryotic":[141],"eukaryotic":[143],"illustrate":[146],"its":[147],"usability.":[148],"AVAILABILITY:":[149],"freely":[153],"available":[154],"at":[155],"http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi.":[156]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
