Codon Usage Robot

This page describes the use of the Codon Usage Robot. If you would like to know how the algorithm works internally please click here.

With Codon-Usage robot, user can analyze the codon usage bias. Codon-Usage robot can be found at likelihoodbot@appspot.com.
Before you start analyzing codon usage bias using this robot, make sure that you have a sequence selected in the workspace.

ORF Selection

After selecting the sequence into workspace, user can specify open reading frame (ORF) parameters. Also user can specify the organism for which the codon usage in the sequence is to be analyzed. Additionally user can specify the start codon for the ORF, otherwise default start codon (ATG) is used.

Codon Usage Finding

So based on the parameters entered by the user, Codon-Usage robot finds all the open reading frames in all the frames first and then highlights all the codons that are not acceptable (which are very less frequent) for the selected organism. The output of the Codon-Usage robot is similar to the the following image. It displays the original sequence, followed by all the open reading frames that are found in a reading frame. Multiple frames found one after the other are also displayed and then all the unacceptable codons are highlighted.

Note: The display may slightly differ from this picture due to ongoing development.

Brief Overview of Algorithm

If the frame number entered by the user is 0 then Codon usage Robot first finds the ORFs in all reading frames and then check them for the rare codons if any corresponding to the selected organism .
It simply traverses through all the reading frames from 1 to 6 one by one.
When it finds the start codon(specific entered by the user or standard ATG) and the corresponding stop codon, it declares that the ORF is found on the reading frame.
Then it searches ahead for more ORFs.
It checks for the presence of rare codons in all the frames and highlights them.