How do I generate a custom Codon Usage Table

MacVector has a Codon Usage Table viewer. You can use this to generate a codon usage table (CUT or .bias) file. You can import data directly from codon usage websites or generate your own by translating CDS features in one or more sequences.

Codon Usage Table viewer

This is a simple viewer for codon usage “.bias” files. This displays the data in a standard text format with one row of data per codon, identical to codon usage output windows used in other MacVector translation functions.

Importing codon usage tables

Select New From Clipboard will create a new CUT file in the Codon Usage Table viewer as long as the text on the clipboard adheres to this format, or to the popular “GCG” format available on codon usage websites such as CUTG (http://www.kazusa.or.jp/codon/).

Generating custom Codon Usage Tables

Generate a CUT from translating CDS in a single sequence.

You can also generate CUTs by translating CDS directly.

1. Open a sequence that has annotated CDS features.
2. Analyze | Translate All CDS Features…
3. Toggle Create Codon Usage Table (.bias) to on and enter a suitable name.
4. Click OK.

Generating Codon Usage Tables from multiple sequences.

Using the CUT viewer

Generating Codon Usage Tables from multiple sequences.

The viewer has a toolbar button for the Translate All CDS Features in Folder function. You can invoke this multiple times and each new set of results will be added to the existing codon usage data. You can use this to slowly build up the codon usage information from a large sequence data set in multiple folder locations on your computer.

1. Start by one of the following methods:
   • File | New | Codon Usage Table (.bias)
   • Click Transl.Folder
   or
   • run Database | Translate All CDS Features in Folder
2. Choose a folder of sequences you want to generate a CUT from.
3. The CUT viewer will be blocked until the job has finished.
4. Click Transl.Folder to repeat this procedure with multiple folders. At each stage the CUT will be updated.

Related Topics.

Symbol editor

Editing the general map appearance

How do I? - videos

Optimizing Codon Usage of a sequence.