Data mining pathogen genomes using GeneOrder and CoreGenes: gene order, synteny, and proteomes

摘要

Genome sequence databases are growing at an exponential rate due to the "next generation" DNA analyzers. These include determining multiple sequences of serovars of previously sequenced organisms, particularly ones of consequence to human health and epidemics. The applications of these sequence data are limited by the tools available to mine them, particularly user-friendly tools that are available to the bench researcher. GeneOrder and CoreGenes are two web-based on-the-fly whole genome tools that can be used to examine gene order and synteny, as well as to catalog proteomes for comparative genomics. A new version of GeneOrder allows and expedites the analysis of genomes ranging up to 4 megabases. Many bacterial pathogens are of this genomic size; for example, validation of this version of the tool is provided by its application to E. coli serovars K12 and O157:H7. The original version already allows the analysis of virus-sized genomes and small bacterial genomes. Other updated options include the ability to enter proprietary and/or unpublished genome data. In addition, the tool is useful for genome annotation, with particular emphasis on the annotation of hypothetical proteins.