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Open Access Technical Note

Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

Padmanabhan Mahadevan12 and Donald Seto1*

Author Affiliations

1 Department of Bioinformatics and Computational Biology, 10900 University Blvd., MSN 5B3. George Mason University, Manassas, VA 20110, USA

2 Current address: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA

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BMC Research Notes 2010, 3:41  doi:10.1186/1756-0500-3-41

Published: 23 February 2010



The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling.


GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations.


The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.