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Team:Freiburg Software/User/Robots/Codon
From 2010.igem.org
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<h1>Codon Usage Robot</h1> | <h1>Codon Usage Robot</h1> | ||
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<img src="https://static.igem.org/mediawiki/2010/5/5a/Freiburg_10_software_Internals.png" width=100/> | <img src="https://static.igem.org/mediawiki/2010/5/5a/Freiburg_10_software_Internals.png" width=100/> | ||
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With Codon-Usage robot, user can analyze the codon usage bias. Codon-Usage robot can be found at likelihoodbot@appspot.com.<br> | With Codon-Usage robot, user can analyze the codon usage bias. Codon-Usage robot can be found at likelihoodbot@appspot.com.<br> | ||
Before you start analyzing codon usage bias using this robot, make sure that you have a sequence selected in the workspace.</p> | Before you start analyzing codon usage bias using this robot, make sure that you have a sequence selected in the workspace.</p> | ||
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<h2>ORF Selection</h2> | <h2>ORF Selection</h2> | ||
Revision as of 20:17, 26 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.
