Skip Navigation


Bioinformatics Advance Access originally published online on February 26, 2004
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/11/1812    most recent
bth159v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (24)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Kerkhoven, R.
Right arrow Articles by Siezen, R. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kerkhoven, R.
Right arrow Articles by Siezen, R. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Applications Note

Visualization for genomics: the Microbial Genome Viewer

Robert Kerkhoven 1,*, Frank H. J. van Enckevort 1,2, Jos Boekhorst 1, Douwe Molenaar 2,3 and Roland J. Siezen 1,2,3

1 Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands, 2 NIZO Food Research, P.O. Box 20, 6710 BA Ede, The Netherlands and 3 Wageningen Centre for Food Sciences (WCFS), P.O. Box 557, 6700 AN Wageningen, The Netherlands

Received on October 14, 2003; accepted on January 7, 2004

Summary: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection.

Availability: The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Contact: R.Kerkhoven{at}cmbi.kun.nl

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S. J. Jones, and M. A. Marra
Circos: An information aesthetic for comparative genomics
Genome Res., September 1, 2009; 19(9): 1639 - 1645.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Liu, R. J. Siezen, and A. Nauta
In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing
Appl. Envir. Microbiol., June 15, 2009; 75(12): 4120 - 4129.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. Wels, R. S. Bongers, J. Boekhorst, D. Molenaar, M. Sturme, W. M. de Vos, R. J. Siezen, and M. Kleerebezem
Large Intergenic Cruciform-Like Supermotifs in the Lactobacillus plantarum Genome
J. Bacteriol., May 15, 2009; 191(10): 3420 - 3423.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Carver, N. Thomson, A. Bleasby, M. Berriman, and J. Parkhill
DNAPlotter: circular and linear interactive genome visualization
Bioinformatics, January 1, 2009; 25(1): 119 - 120.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. W. W. Brouwer, S. A. F. T. van Hijum, and O. P. Kuipers
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Bioinformatics, January 1, 2009; 25(1): 139 - 140.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. J. G. van de Werken, M. R. A. Verhaart, A. L. VanFossen, K. Willquist, D. L. Lewis, J. D. Nichols, H. P. Goorissen, E. F. Mongodin, K. E. Nelson, E. W. J. van Niel, et al.
Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus
Appl. Envir. Microbiol., November 1, 2008; 74(21): 6720 - 6729.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. R. Grant and P. Stothard
The CGView Server: a comparative genomics tool for circular genomes
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W181 - W184.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. L. Marco, R. S. Bongers, W. M. de Vos, and M. Kleerebezem
Spatial and Temporal Expression of Lactobacillus plantarum Genes in the Gastrointestinal Tracts of Mice
Appl. Envir. Microbiol., January 1, 2007; 73(1): 124 - 132.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
T. Koessler, P. Francois, Y. Charbonnier, A. Huyghe, M. Bento, S. Dharan, G. Renzi, D. Lew, S. Harbarth, D. Pittet, et al.
Use of Oligoarrays for Characterization of Community-Onset Methicillin-Resistant Staphylococcus aureus.
J. Clin. Microbiol., March 1, 2006; 44(3): 1040 - 1048.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Pritchard, J. A. White, P. R.J. Birch, and I. K. Toth
GenomeDiagram: a python package for the visualization of large-scale genomic data
Bioinformatics, March 1, 2006; 22(5): 616 - 617.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. W. E. J. Fiers, H. van de Wetering, T. H. J. M. Peeters, J. J. van Wijk, and J.-P. Nap
DNAVis: interactive visualization of comparative genome annotations
Bioinformatics, February 1, 2006; 22(3): 354 - 355.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
B. Teusink, F. H. J. van Enckevort, C. Francke, A. Wiersma, A. Wegkamp, E. J. Smid, and R. J. Siezen
In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments
Appl. Envir. Microbiol., November 1, 2005; 71(11): 7253 - 7262.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Stothard and D. S. Wishart
Circular genome visualization and exploration using CGView
Bioinformatics, February 15, 2005; 21(4): 537 - 539.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.