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Bioinformatics Vol. 17 no. 2 2001
Pages 162-166
© 2001 Oxford University Press

Original Paper

GeneOrder: comparing the order of genes in small genomes

Raja Mazumder 1, Ashok Kolaskar 2 and Donald Seto 1,*

1 School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110, USA
2 Bioinformatics Program, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110, USA

Received on July 8, 2000 ; revised on October 9, 2000 ; accepted on November 21, 2000

Motivation: The recent rapid rise in the availability of whole genome DNA sequence data has led to bottlenecks in their complete analysis. Specifically, there is a need for software tools that will allow mining of gene and putative gene data at a whole genome level. These new tools will complement the current set already in use for studying specific aspects of individual genes and putative genes in detail. A key software challenge is to make them user-friendly, without losing their flexibility and capability for use in research.

Results: The creation of GeneOrder—a web-based interactive, computational tool—allows researchers to compare the order of genes in two genomes. It has been tested on full genome sequence data for viruses, mitochondria and chloroplasts that were obtained from the NCBI GenBank database. It is accessible at http://www.bif.atcc.org/GENEOrder/index.html. GeneOrder prepares the comparison in table form, listing the order of similar genes. Hyperlinks are provided from this output; these lead to the ‘Protein Coding Regions’ in the NCBI database.

* To whom correspondence should be addressed.


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