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CSE 490MT: Starting gene(s) |
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For now, as the starting gene for this first phase of
your project, all teams should use folC in Bacillus subtilis.
Here is its protein table entry:
2864573..2865865 - 431 16079860 folC COG0285 Bsu2804 folyl-polyglutamate synthetaseThe reason to have all 3 teams start with the same gene is just so that you can compare files with each other for debugging purposes. For instance, your files of upstream sequences should turn out similar to each other: they will differ only in how many homologous genes you decide to use, and how you resolve small issues such as handling operons. But, for instance, you will all decide to include folC in Listeria innocua as a homologous gene (it's #4 on the BLAST list), and your upstream sequences for this gene should all agree in their last (3' end) few hundred nucleotides. Similarly, you can compare the amino acid sequences of this gene's protein product for debugging purposes. Once you are confident that your programs are working correctly, I'll suggest different starting genes (and eventually starting families of genes) for the 3 projects. The starting place for identifying genes of interest will be the BioCyc Pathways Databases, which we will discuss later. |
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