====== Backtranslation ======
The backtranslation feature automatically selects codons to encode an amino acid sequence.
    * Gene Designer 2.0 uses a genetic algorithm to avoid getting stuck in suboptimal local minima.
    * Gene Designer 2.0 uses parameters that are stored in a backtranslation profile to guide its choice of codons.


===== Backtranslation Profiles =====
=== Creating a backtranslation profile ===
Backtranslation profiles can be created and edited by selecting "Backtranslation Profiles" from the "Configure" pull-down menu at the top of the [[ui:Construct Editor]]
  * This will open a window giving you the option of adding, editing or removing a profile.
  * By storing backtranslation profiles you can use the same parameters for many constructs without having to re-enter the same data every time.
{{:guide:backtranslation_profile1.jpg}}
=== Editing a backtranslation profile ===
All backtranslation profiles can be viewed and edited from the Configure: Backtranslation Profiles menu
  * The backtranslation profile for a construct can be viewed but not edited in the [[ui:Details View]]

=== Backtranslation parameters ===

  * The backtranslation profile allows you to control:

== The genetic algorithm == 
      * Genetic algorithm parameters default to the values that DNA2.0 uses in-house.  
      * If you want to modify them, feel free to play around, or contact DNA2.0 for help.

== The codon bias table used ==
      * Codon bias tables can be dragged in out of the [[ui:Codon Table Library]] in the [[ui:Library Explorer]]
      * A threshold value can also be set for codon selection, by selecting the "Edit Threshold" button.
        * Codons that appear in the codon table selected at a lower frequency than the threshold value set will not be included in the design
        * Threshold values are frequencies, and must be between 0 and 1.

== Unwanted sequences that will be excluded from backtranslated sequences ==
Sequences to exclude from backtranslated sequences can be modified by selecting the "Edit Unwanted Sequences" button.
  * Unwanted sequences can easily be added from your [[guide: managed lists]] of restriction enzymes or motifs
  * Examples of sequences that can be excluded from backtranslated sequences include
    * restriction sites 
    * sequence motifs
      * cryptic splice sites
      * ribosome binding sites
      * cryptic termination sites

== Repeats ==
      * The size of repeats that the software attempts to eliminate.
{{:guide:backtranslation_profile2.jpg}}
===== Backtranslating a Construct =====
Backtranslation of a construct is done by selecting "Back Translate" from the Tools Menu.
  * You can select the construct to backtranslate.
  * You can select the ORFs within that construct to backtranslate.
    * If an ORF has manually fixed codons, you can choose to clear these codons.
  * You can select which backtranslation profile is used, by choosing either:
    * The profile that was used the last time you backtranslated this construct.
    * A profile taken from your profile manager.
{{:guide:backtranslate.jpg}}