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Bioinformatics Advance Access published online on February 26, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth159
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 14, 2003
Accepted January 7, 2004

Applications note

Visualization for genomics: the Microbial Genome Viewer

Robert Kerkhoven 1*, Frank H. J. van Enckevort 2, Jos Boekhorst 1, Douwe Molenaar 3, Roland J. Siezen 4

1 1Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
2 1Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands; 2NIZO Food Research, P.O. Box 20, 6710 BA Ede, The Netherland
3 2NIZO Food Research, P.O. Box 20, 6710 BA Ede, The Netherlands; 3Wageningen Centre for Food Sciences (WCFS), P.O. Box 557, 6700 AN Wageningen, The Netherlands
4 1Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands; 2NIZO Food Research, P.O. Box 20, 6710 BA Ede, The Netherlands; 3Wageningen Centre for Food Sciences (WCFS), P.O. Box 557, 6700 AN Wageningen, The Netherlands

* To whom correspondence should be addressed. E-mail: R.Kerkhoven{at}cmbi.kun.nl.


  Abstract

Summary: A web-based visualization tool, the Microbial Genome Viewer, is presented which 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


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