## Codon Statistics Quick Start

**What is it?**Codon Statistics (CS) is a java based user interface, which enables one to quickly browse statistical information on one or more genomes. One may view statistical information on both graphical and tabular forms.

**How do I get started?**

- Select Codon Statistics from the
*VBRC Tools*drop-down menu (top left of page). - Click the Launch Program button. CS will be downloaded to your computer and Java Web Start will automatically start the program.
- Choose the database of interest from the list that appears.

Click here to go directly to the CS page.

**What next? **The main CS window shown below will open.

Once you have selected a genome, the following will open:

Once you have selected one or more genes, additional information is shown:

The codon table displays the percentage of each nucleotide in each codon position. a_1 represents the number of a’s occurred in the first position of a codon divided by the length of the gene; similarly to other column. In the bottom of the table, the sum, mean, and the variance are displayed, which are the statistical data of the set of genes.

**The mean is calculated by the formula of:** Mean = Sum/number of genes selected

**The variance is estimated by the formula of:** Var = sum of(yi-Mean)^2 /(number of genes -1) Where yi is the ith gene in the table and i from 1 to the number of genes.

**95% CI Low Bound** = Mean-1.96 sqrt(Var/N)

**Up Bound** = Mean + 1.96 sqrt(Var/N)

When N>=100, the 95%CI values can be used safely. Otherwise, normality testing is needed before using the data.

From the **Genes View** window, users can view line and bar graphs of the relative nucleotide codon compositions: