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Center for Nonlinear Studies |
In 1995, two bacterial genomes were published, and starting with these two genomes, comparative genomics was possible. Now, at the end of 2012, there are roughly 20,000 bacterial genomes that are publicly available to compare, and the cost of sequencing a bacterial genome is continuing to become more economical. There is hope that with 'third generation sequencing', it will be possible to get high-quality finished bacterial genome sequences in a few minutes. Dealing with too much data can be a daunting task. There are many methods to compare bacterial genomes, including simple statistics of quantities such as genome size, number of protein-encoding genes, rRNA operons, tRNAs, etc. More complicated methods can compare sets of conserved core-genes and the collection of all genes (the 'pan-genome') for a given set of genomes, as well as predicted metabolic properties. The AT content of a genome can vary along the chromosome, and for more than 2000 complete bacterial genomes studied, the intergenic regions are consistently about 5% more AT rich, regardless of the %AT of the genome. Further, A's (and G's) tend to be bias towards the replication leading strand in Gram positives, whilst the A's (but not G's) are bias towards the lagging strain in Gram negatives. Finally, it is possible, based on a genome sequence, to make an educated guess as to the taxonomy of the organism, and currently methods are being developed for high-throughput genome-based molecular typing of bacterial genomes.
Host: Brian Foley, T-6 btf@lanl.gov