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Team:Freiburg Software/User/Robots/Translation
From 2010.igem.org
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<li>If the frame number entered by the user is 0 then TranslationBot finds the ORFs in all reading frames. </li> | <li>If the frame number entered by the user is 0 then TranslationBot finds the ORFs in all reading frames. </li> | ||
| - | <li>It simply traverses through all the reading frames from 1 to 6 one by one.</li> <li>When it finds the start codon(ATG) and the corresponding stop codon, it declares that the ORF is found on the reading frame. </li><li>Then it searches ahead for more ORFs.</li> <li>Then it translates all the ORFs found on each frame. In other words, it matches the corresponding amino acid for the corresponding DNA triplet in the ORF using the <a href="http://en.wikipedia.org/wiki/DNA_Codon_Table">DNA Codon Table </a>and forms the protein sequence from it.</li> | + | <li>It simply traverses through all the reading frames from 1 to 6 one by one.</li> <li>When it finds the start codon(ATG) and the corresponding stop codon, it declares that the ORF is found on the reading frame. </li><li>Then it searches ahead for more ORFs.</li> <li>Then it translates all the ORFs found on each frame. In other words, it matches the corresponding amino acid for the corresponding DNA triplet in the ORF using the <a href="http://en.wikipedia.org/wiki/DNA_Codon_Table" target="_blank">DNA Codon Table </a>and forms the protein sequence from it.</li> |
</ul> | </ul> | ||
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Revision as of 21:30, 26 October 2010
Translationbot
This page describes the use of the Translation Robot. If you would like to know how it works internally please click here.
With Translation robot, user can translate DNA sequences or BioBrick parts into Protein sequences. Translation robot can be found at translate-beta@appspot.com.
Before you start translation make sure that you have a sequence selected in the workspace to translate it into protein.
ORF Selection
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.
Translation
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.
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 TranslationBot finds the ORFs in all reading frames.
- It simply traverses through all the reading frames from 1 to 6 one by one.
- When it finds the start codon(ATG) and the corresponding stop codon, it declares that the ORF is found on the reading frame.
- Then it searches ahead for more ORFs.
- Then it translates all the ORFs found on each frame. In other words, it matches the corresponding amino acid for the corresponding DNA triplet in the ORF using the DNA Codon Table and forms the protein sequence from it.
