GeneOrder: comparing the order of genes in small genomes

Motivation: The recent rapid rise in the availability of whole genome DNA s equence data has led to bottlenecks in their complete analysis. Specificall y, there is a need for software tools that will allow mining of gene and pu tative gene data at a whole genome level. These new tools will complement t he current set already in use for studying specific aspects of individual g enes 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 t ool-allows researchers to compare the order of genes in two genomes. It has been tested on full genome sequence data for viruses, mitochondria and chl oroplasts that were obtained from the NCBI GenBank database. It is accessib le at http://www.bif.atcc.org/GENEOrder/index.html. GeneOrder prepares the comparison in table form, listing the order of similar genes. Hyperlinks ar e provided from this output; these lead to the 'Protein Coding Regions' in the NCBI database.