Genome Project Solutions

For the month of January and February, 2010, the two posters we presented at the Plant and Animal Genomes Conference will be available here.

Poster 1 (Click here to download): 

Will Your Favorite Genome Be Sequenced?

The past decade has seen a fantastic acceleration in our ability to sequence complete genomes. We anticipate that this exponential increase will continue for at least the next several years. Will your favorite genome be sequenced? We review the several technologies that are state-of-the-art for genome sequencing, describe their capabilities, provide an interpretation of the pros and cons of each and argue for the most appropriate mix of techniques for whole genome sequencing. We describe the factors important in the choice of genomes to target, the current potential for funding such a large project and the options for follow-on analyses that will maximize biological discovery and the utility of the work to the broader scientific community.

Poster 2 (Click here to download): 

Evolutionary Analysis As The Basis For Interpreting, Comparing, And Presenting Genomes: The GATOR And PHRINGE System

We anticipate a great acceleration in whole genome sequencing over the next few years. Current tools for interpreting, comparing, and presenting these data cannot handle the expected pace, lack integration, require extensive IT support and computational expertise, and do too little to facilitate biological discovery. In particular, the standard “browser” format is anachronistic, with the genome assembly, rather than the biological information, being the organizing principle. It requires great manual effort to identify any particular gene or biochemical pathway. Fortunately, two new developments are enabling a better approach. First, next generation sequencing technology allows very deep sequence coverage of the set of expressed genes. For example, 200-fold mean sequence coverage can be obtained on a typical transcriptome for about $20,000. This means that genes can be modeled with much greater accuracy, so even the early stages of analysis can focus on biological discovery instead of manual gene curation. Second, we have developed an effective tool (“PHRINGE”, for Phylogenetic Resources for Interpreting Genomes) for assigning orthologous and paralogous relationships among genes based on phylogenetic analysis of complete gene sets. In the absence of biochemical characterization, the best inference of gene function is by inferring that orthologous genes retain the same function. This is incorporated into the “GATOR” (Genome Analysis Tools and Online Resources) system under development, a “gene-centric”, user-friendly, streamlined approach to genome interpretation, comparison, and presentation. The entry point is the gene catalog itself, sortable by many categories, including domain content, intracellular location, SNP content, biochemical pathway, protein characteristics, number of members in any gene family, and many others. Users can view evolutionary trees, gene colinearity maps, and links to protein structures for all genes in multiple sequenced genomes.