Codon usage table analysis

This tool analyzes codon usage tables and lists the relative usage of codons for each amino acid.

Quick start

Just enter the codon usage table you want to use, then press the “Start Analysis” button. You can get ready-to-use codon usage tables for many species from the codon usage database. See below the tool for detailed instructions.

Purpose of this applet

This Java applet analyzes a codon usage table. Such a table contains all possible codons (all combinations of three nucleotides, 64 in total) along with their relative usage in a genome, or a genome subset. Codon usage tables are computed from large gene databases, usually for a certain species or tissue.

The applet creates a list of all 20 amino acids, and shows for each amino acid, which codon encodes which relative amount of amino acids of this type. Example:

   A (Alanine):
   GCU: 5.955 % GCC: 35.588 % GCA: 10.147 % GCG: 48.308 %

Here, GCU codes for 5.955% of all alanines, GCC for 35.588%, and so on. This format is much easier to interpret than the usual codon usage tables. However, please note that it contains less information, since the relative usage of different amino acids is lost.

Codon usage table

This is either a DNA sequence or a list of codons, followed by a decimal number. The decimal number
denotes the relative usage of the respective codon compared to all other codons, e.g.

    UUU 0.12

indicates that the codon UUU (encoding phenylalanine) is used in 12% of all codons. The ratio values can add up to any amount (e.g. 1.0, 100.0, 347.5), since the applet rescales them to a sum of 1.0 for all codons encoding the same amino acid.

Example

The codons UCU (2.0), UCC (10.1), UCA (4.1), UCG (8.1), ACU (0.0), and AGC (12.2) all encode serine, with the given relative occurrences (out of 1000) in a certain genome. This means UCU is used in 2 out of 1000 codons. The applet calculates now how often UCU, UCC, … AGC are used to encode serine. In our example, this would mean that UCU is used to encode 5.5% of all serines, UCC to encode 27.7%, and so on. A codon usage table with these values would therefore result in a backtranslated nucleotide sequence, where the codon UCC is used in 27.7% of all cases in which a serine is encoded.

Start analysis

After you have pasted a codon usage table, please click on this button to start the analysis. If there are any errors, they will be displayed in the field “Result of the analysis”. You can also exclude certain codons from being used by either omitting them, or by placing a “-” (minus) right before them (e.g. “-UCC”). The applet ignores all additional characters such as brackets. Therefore, codon usage tables from the codon usage database can be used unmodified.

Result of the analysis

This field will contain the transformed codon usage table. You can select it and copy it to the clipboard or print it out.

If there have been any errors during the analysis, this field will contain the corresponding error message(s).