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Open Access Software

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes

Srikanth Celamkoti1, Sashidhara Kundeti1, Anjan Purkayastha1, Raja Mazumder2, Charles Buck3 and Donald Seto1*

  • * Corresponding author: Donald Seto

  • † Equal contributors

Author Affiliations

1 Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University. 10900 University Boulevard, MSN 5B3, Manassas, VA 20110 USA

2 Biochemistry and Molecular Biology Department, Georgetown University School of Medicine. 4000 Reservoir Road, Washington, D.C. 20057 USA

3 Virology Program, American Type Culture Collection (ATCC). 10801 University Boulevard, Manassas, VA 20110, USA

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BMC Bioinformatics 2004, 5:52  doi:10.1186/1471-2105-5-52

Published: 5 May 2004



An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb.


GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.


GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." Availability: webcite and webcite.