Team:Freiburg Software/User/Robots/Codon

From 2010.igem.org

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<h2>ORF Selection</h2>
<h2>ORF Selection</h2>
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After selecting the sequence into workspace, user can specify open reading frame (ORF) parameters. Tranlsation robot finds the open reading frames in all the reading frames or a particular specified frame and translates it into the protein sequence. So user specifies a particular frame (1..6) or 0 to find ORFs in all reading frames. Also the user can specify minimum length of the open reading frame to find, so all the frames of equal or more length are extracted.
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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.
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<h2>Codon Usage Finding</h2>
<h2>Codon Usage Finding</h2>
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So based on the parameters entered by the user, Translationbot finds all the frames and translates them. The output of the translation can be as displayed in 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.  
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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.  
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Revision as of 17:34, 23 October 2010

Codon Usage Robot

This page describes the use of the Codon-Usage Robot. If you would like to know how it 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.

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