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Team:Alberta/Project/Bioinformatics
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Revision as of 02:49, 11 September 2009
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Why build a minimal genome?Genomes are complex! Determining how simplified a genome can become enriches our understanding the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology. |
Presentations
The size and complexity of the genome make bioinformatics analysis essential. We used bioinformatics to accomplish the following:
- review lists of essential genes in the literature and existing databases and compile a preliminary essential gene list - model the metabolic reactions and net growth rate of E.coli with given gene sets. This identified additional metabolic genes essential to a minimal genome. - identify knock out combinations that could be tested in the wet lab, to verify the accuracy of our metabolic model. - select standardized promoters and terminators that would replace the natural promoters and terminators of essential genes. - determine which promoter should be used with which gene, by analyzing expression level data. - design primers to amplify all essential genes from genomic DNA. These steps have all been completed, and are described on the following pages.
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