Generate a codon usage table

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Using OrganismView to generate a codon usage table. 1. search for organism. 2. click "click for features" under genome information. 3. click "click for codon usage table"
Codon usage tbale for Alkalilimnicola ehrlichei strain MLHE-1
Amino acid usage tbale for Alkalilimnicola ehrlichei strain MLHE-1

It is easy to create a codon usage table in CoGe.

  1. Go to OrganismView and find your organism of interest. For example, try Alkalilimnicola ehrlichei strain MLHE-1, a high GC content gammaproteo bacteria isolated from Mono lake in California.
  2. If you need to select a particular version of a genome, do so.
  3. Click "click for features" link under "Genome information". This will generate a summary table of all the genomic features in a genome and show the table below.
  4. If there are CDS features in the genome, a link will be shown below the feature table called "click for codon usage table". Click this link and a dialog box will appear saying that the codon usage table is being generating. Depending on the number of CDS features in the genome, this may take a couple of sequences to several minutes. When the tabulation is finished, the codon usage table will appear in this dialog box.

Note: You can generate an amino acid usage table by following the same steps and following the link called "click for amino acid usage table" located below the one for generating the codon usage table. A new dialog box will appear with this table in it. Thus, both can be shown at the same time.