The University of Georgia is awarded a grant to investigate the significance of microbial genome features beyond the protein-coding and RNA-coding genes. Standard computational analyses of genomes center on genes and gene content, whereas the availability of software to analyze other genomic features is limited. Investigating the full range of genomic features is important to understand the mechanisms of genome evolution and function. Genome features of interest include global and local characteristics. Global features range from very simple, such as G+C content, through species-specific preferences in codon usage, amino acid usage, and oligonucleotide composition, to cryptic periodic signals related to DNA curvature and nucleoid structure. Local features include, for example, specific sequence motifs and repeat structures (e.g., simple sequence repeats, palindromes, close repeats, or various types of short dispersed repeats), sequence patterns that can promote unusual DNA conformations (e.g., Z-DNA, H-DNA, G-DNA), or sequences that locally affect physical characteristics of DNA or RNA molecules (e.g., stability, curvature). Direct evidence of biological significance of these genome features is scarce. With limited experimental options, the detection of biologically significant genomic features often relies on statistical methods. Computational tools will be designed for analyses of these features in microbial genomes, and subsequently these tools will be applied in systematic examination of prokaryotic genomes. Comparative genomic approaches will be used for initial validation of the results obtained by statistical analyses of individual genomes and some of the specific hypotheses will be verified by experiments. The data ensuing from the comparative analyses of microbial genomes will be available to other researchers and can be utilized in interpretations of experimental data and design of future experiments.
A significant part of this project is devoted to enhancing research infrastructure by developing new computational methods, algorithms and tools for analyses and comparisons of microbial genomes. The new software will be distributed under the terms of the GNU General Public License, which allows anyone to use and modify the software without restrictions. In addition to making software available for download, interactive user interfaces will be developed and combined in an online environment for analysis of prokaryotic genomes. Software developed in this project will be used in courses and workshops. Undergraduate and high school students will be recruited to participate in the research. This effort includes a new student-parent summer program, where high school or undergraduate students will execute a research project together with a parent or other relative. Furthur information about this project and its software may be found at the PI's lab website at www.cmbl.uga.edu/.
