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 can be created and edited by selecting “Backtranslation Profiles” from the “Configure” pull-down menu at the top of the 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.

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 Details View

• The backtranslation profile allows you to control:

• 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.

• Codon bias tables can be dragged in out of the Codon Table Library in the 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.

Sequences to exclude from backtranslated sequences can be modified by selecting the “Edit Unwanted Sequences” button.

• Unwanted sequences can easily be added from your 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

• The size of repeats that the software attempts to eliminate.

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.