CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb

CGUG is available at http://binf.gmu.edu/geneorder.html webcite as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes.CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.There is a tremendous increase in the number of genomes deposited in databases, with the data stream already a "data tsunami". The universal adoption of the "Next Generation" DNA sequencing technologies will also allow a parallel, expedited sequencing of smaller, but important and relevant, genomes such as from viruses and less than 2 Mb bacterial genomes.Software tools for taking advantage of these data need to be developed as well as maintained and upgraded for additional and more useful functions. In particular, the readily available and "user-friendly" computational tools, preferably platform-independent, are especially needed as many wet-bench researchers are interested in the informational content, the "biology," of the genomes rather than the computational aspects of these genomes.CGUG is a modification and extension of a web-based tool, CoreGenes [1], which was limited to genomes of viruses (ca. 350 kb), including chloroplasts and mitochondria. It now determines the "core" set of genes from a set of up to five bacteria with