{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T00:32:57Z","timestamp":1774053177185,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.<\/jats:p>\n               <jats:p>Results: Here, we present two complementary approaches to tackle this problem. First, we propose the SuperGenome concept for the computation of a common coordinate system for all genomes in a multiple alignment. This coordinate system allows for the consistent placement of genome annotations in the presence of insertions, deletions and rearrangements. Second, we present the GenomeRing visualization that, based on the SuperGenome, creates an interactive overview visualization of the multiple genome alignment in a circular layout. We demonstrate our methods by applying them to an alignment of Campylobacter jejuni strains for the discovery of genomic islands as well as to an alignment of Helicobacter pylori, which we visualize in combination with gene expression data.<\/jats:p>\n               <jats:p>Availability: GenomeRing and example data is available at http:\/\/it.inf.uni-tuebingen.de\/software\/genomering\/<\/jats:p>\n               <jats:p>Contact: \u00a0kay.nieselt@uni-tuebingen.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts217","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i7-i15","source":"Crossref","is-referenced-by-count":42,"title":["GenomeRing: alignment visualization based on SuperGenome coordinates"],"prefix":"10.1093","volume":"28","author":[{"given":"A.","family":"Herbig","sequence":"first","affiliation":[{"name":"Center for Bioinformatics T\u00fcbingen, Faculty of Science, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"G.","family":"J\u00e4ger","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics T\u00fcbingen, Faculty of Science, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"F.","family":"Battke","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics T\u00fcbingen, Faculty of Science, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"K.","family":"Nieselt","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics T\u00fcbingen, Faculty of Science, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512394024900_B1","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"2023012512394024900_B2","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/1471-2105-11-121","article-title":"Mayday \u2013 Integrative analytics for expression data","volume":"11","author":"Battke","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512394024900_B3","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1517\/14622416.5.4.433","article-title":"Solexa ltd","volume":"5","author":"Bennet","year":"2004","journal-title":"Pharmacogenomics"},{"key":"2023012512394024900_B4","doi-asserted-by":"crossref","first-page":"1566","DOI":"10.1086\/315855","article-title":"Identification of loci essential for the growth ofHelicobacter pyloriunder acidic conditions","volume":"182","author":"Bijlsma","year":"2000","journal-title":"J. Infect. Dis."},{"key":"2023012512394024900_B5","author":"Broad Institute","year":"2009","journal-title":"MEDEA comparative genomic visualization with Adobe Flash."},{"key":"2023012512394024900_B6","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1053\/j.gastro.2009.01.073","article-title":"Helicobacter pyloriin health and disease","volume":"136","author":"Cover","year":"2009","journal-title":"Gastroenterology"},{"key":"2023012512394024900_B7","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"2023012512394024900_B8","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS One"},{"key":"2023012512394024900_B9","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.jbiotec.2008.03.021","article-title":"The Genome Sequencer FLX System\u2013longer reads, more applications, straight forward bioinformatics and more complete data sets","volume":"136","author":"Droege","year":"2008","journal-title":"J. Biotechnol."},{"key":"2023012512394024900_B10","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"Durbin","year":"2010","journal-title":"Nature"},{"key":"2023012512394024900_B11","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"2023012512394024900_B12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0030015","article-title":"Major structural differences and novel potential virulence mechanisms from the genomes of multipleCampylobacterspecies","volume":"3","author":"Fouts","year":"2005","journal-title":"PLoS Biol."},{"issue":"Suppl. 2","key":"2023012512394024900_B13","doi-asserted-by":"crossref","first-page":"W273","DOI":"10.1093\/nar\/gkh458","article-title":"VISTA: computational tools for comparative genomics","volume":"32","author":"Frazer","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512394024900_B14","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0882-4010(90)90048-U","article-title":"Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extra intestinalEscherichia coliisolates","volume":"8","author":"Hacker","year":"1990","journal-title":"Microbial Pathogenesis"},{"key":"2023012512394024900_B15","first-page":"261","article-title":"ColorBrewer.org: an online tool for selecting colour schemes for maps","author":"Harrower","year":"2003","journal-title":"The Map Reader"},{"key":"2023012512394024900_B16","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/jhered\/esp086","article-title":"Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species","volume":"100","author":"Haussler","year":"2009","journal-title":"J. Hered."},{"key":"2023012512394024900_B17","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"2023012512394024900_B18","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1109\/TVCG.2009.167","article-title":"MizBee: A multiscale synteny browser","volume":"15","author":"Meyer","year":"2009","journal-title":"Visualization Comput. Graph. IEEE Trans."},{"key":"2023012512394024900_B19","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1038\/nmeth.1422","article-title":"Visualizing genomes: techniques and challenges","volume":"7","author":"Nielsen","year":"2010","journal-title":"Nat. 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Appl. Microbiol."},{"key":"2023012512394024900_B26","first-page":"115","article-title":"Integrative systems biology visualization with MAYDAY","volume":"7","author":"Symons","year":"2010","journal-title":"J. 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