User GuidesSnapGene User Guide Codon UsageImport or Create a Codon Usage Table

Import or Create a Codon Usage Table

How do I import or create a codon usage table for use in SnapGene?

Custom codon usage tables can be used for

Reverse translation (back translation) - see Make a Protein Sequence from a DNA Sequence

Codon Optimization - see Change Codons in a Coding Sequence (CDS) Based on a Codon Usage Table

Select, Import or Create a Custom Codon Usage Table

Click Tools → Manage Codon Usage Tables.

You can also manage codon usage tables by these methods:

View a protein sequence and choose: Actions → Reverse Translate a Protein, then click Please choose a codon Usage table → Manage Codon Usage Tables

or

View a DNA or RNA sequence, select a CDS and choose: Features → Codons → Choose Alternative Codons, then click Codon Usage Table → Manage Codon Usage Tables

Import a Table from KAZUSA

Click Import/Export → Import Table from Codon Usage Database. Select this option to import a table from https://www.kazusa.or.jp/codon/.

Note that not all codon usage tables available from KAZUSA are ideal for codon usage optimization. We recommend consulting the literature for advice on the appropriate codon usage table to use with your target heterologous host."

Import a Table from an XML File

Click Import/Export → Import Table from File....

In the File chooser locate and select the custom codon usage file, then click Open.

A Custom codon usage XML text document should be formatted as shown below with a list of 64 synonymous codon "frequencies."

<?xml version="1.0" encoding="UTF-8"?>
<CodonUsageTables>
  <UsageTable type="A" name="Trichoderma reesei PHX" speciesID="51453" geneticCode="1" frequencies="GCA:0.023;GCC:0.685;GCG:0.1;GCT:0.193;TGC:0.91;TGT:0.09;GAC:0.845;GAT:0.155;GAA:0.08;GAG:0.92;TTC:0.78;TTT:0.22;GGA:0.035;GGC:0.694;GGG:0.028;GGT:0.243;CAC:0.925;CAT:0.075;ATA:0.007;ATC:0.723;ATT:0.27;AAA:0.03;AAG:0.97;CTA:0.013;CTC:0.465;CTG:0.413;CTT:0.06;TTA:0.007;TTG:0.042;ATG:1;AAC:0.915;AAT:0.085;CCA:0.025;CCC:0.71;CCG:0.123;CCT:0.143;CAA:0.04;CAG:0.96;AGA:0.023;AGG:0.088;CGA:0.107;CGC:0.453;CGG:0.093;CGT:0.235;AGC:0.19;AGT:0.018;TCA:0.018;TCC:0.451;TCG:0.181;TCT:0.141;ACA:0.03;ACC:0.578;ACG:0.218;ACT:0.175;GTA:0.003;GTC:0.719;GTG:0.118;GTT:0.16;TGG:1;TAC:0.93;TAT:0.07;TAA:0.4;TAG:0.3;TGA:0.3"/>
</CodonUsageTables>

 

The newly imported window will appear in the "Manage Codon Usage Tables" window.

Manually Enter a Custom Codon Usage Table

Click Add Table.

Click the "Genetic Code" dropdown to set the genetic code to use with the codon usage table.

Click within the "Codon Usage Table" field to add a name for your custom codon usage table.

Manually add frequency information for all possible codons. Click within the fields provided and enter a frequency value for each codon. The combined values for synonymous codons should add up to 1 (one).

Once all values are entered, click OK.

The manually entered table will appear in the "Manage Codon Usage Tables" window.

Create a Codon Usage Table from one or more CDS sequences

You can also create and save your own custom codon usage table derived from a set of of coding sequences. For more information, see the lesson on Show Codon Frequencies.