{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:40:21Z","timestamp":1675197621079},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability.<\/jats:p>\n               <jats:p>Availability: Our software is freely available at http:\/\/cgcv.cgb.indiana.edu\/cgi-bin\/index.cgi.<\/jats:p>\n               <jats:p>Contact: \u00a0dongq@indiana.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp078","type":"journal-article","created":{"date-parts":[[2009,2,11]],"date-time":"2009-02-11T03:02:45Z","timestamp":1234321365000},"page":"956-957","source":"Crossref","is-referenced-by-count":4,"title":["A web-based software system for dynamic gene cluster comparison across multiple genomes"],"prefix":"10.1093","volume":"25","author":[{"given":"Kashi Vishwanath","family":"Revanna","sequence":"first","affiliation":[{"name":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vivek","family":"Krishnakumar","sequence":"additional","affiliation":[{"name":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qunfeng","family":"Dong","sequence":"additional","affiliation":[{"name":"Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,2,9]]},"reference":[{"key":"2023013110165753300_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B2","doi-asserted-by":"crossref","first-page":"D25","DOI":"10.1093\/nar\/gkm929","article-title":"GenBank","volume":"36","author":"Benson","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B3","doi-asserted-by":"crossref","first-page":"D296","DOI":"10.1093\/nar\/gkh031","article-title":"coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics","volume":"32","author":"Chaudhuri","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B4","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-9-170","article-title":"PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes","volume":"9","author":"Fong","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013110165753300_B5","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkn828","article-title":"Ensembl 2009","volume":"37","author":"Hubbard","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B6","first-page":"1727","article-title":"Operon: a group of genes with the expression coordinated by an operator","volume":"250","author":"Jacob","year":"1960","journal-title":"C. R. Hebd. Seances Acad. Sci."},{"key":"2023013110165753300_B7","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1007\/s002390010184","article-title":"The closest BLAST hit is often not the nearest neighbor","volume":"52","author":"Koski","year":"2001","journal-title":"J. Mol. Evol."},{"key":"2023013110165753300_B8","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1126\/science.1132040","article-title":"Genomic evolution of Hox gene clusters","volume":"313","author":"Lemons","year":"2006","journal-title":"Science"},{"key":"2023013110165753300_B9","doi-asserted-by":"crossref","first-page":"D528","DOI":"10.1093\/nar\/gkm846","article-title":"The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions","volume":"36","author":"Markowitz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B10","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1093\/nar\/29.1.123","article-title":"The comprehensive microbial resource","volume":"29","author":"Peterson","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023013110165753300_B11","doi-asserted-by":"crossref","first-page":"11405","DOI":"10.1073\/pnas.201392198","article-title":"Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH","volume":"98","author":"Rodriguez-Trelles","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110165753300_B12","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1186\/1471-2105-7-472","article-title":"CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes","volume":"7","author":"Uchiyama","year":"2006","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/956\/48984257\/bioinformatics_25_7_956.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/956\/48984257\/bioinformatics_25_7_956.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:21:50Z","timestamp":1675196510000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/7\/956\/210674"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,9]]},"references-count":12,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2009,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp078","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,4,1]]},"published":{"date-parts":[[2009,2,9]]}}}