Table of Contents
Details View
- The Details View allows you to view and edit parameters that are associated with a construct. These are
- Whether the construct is circular or linear
- The position of the origin of a circular construct
- The backtranslation profile
- The Details View also allows you to generate reports about your construct
Backtranslation Summary Report
- The Backtranslation Summary provides a text file for any construct within a project, containing:
- DNA sequence of
- the whole construct
- each element
- A translational map of each Amino Acid element
- A list of occurrences of motifs and restriction sites that were set to avoid during backtranslation
- A list of repeats greater in length than those used during backtranslation
- GC content of the construct
- Notes
Viewing / Editing Construct Parameters
Converting between linear and circular
- A construct can be converted from circular to linear by right clicking on the construct icon and selecting “convert to linear”. (Not yet working in beta version)
- The origin of the circle will become the left-most base in the linear construct.
- A construct can be converted from linear to circular by right clicking on the construct icon and selecting “convert to circular”. (Not yet working in beta version)
- The left-most base in the linear construct will become the origin of the circle.
- A construct can be converted from circular to linear by right clicking on the “Edit” button in the Details View and then checking (or unchecking) the “Circular” box.
Changing the position of the origin
- The origin of a circular construct must be at the beginning of one of its component sequence elements.
- The origin can be changed by by right clicking on the construct icon and selecting “change origin”. (Not yet working in beta version)
- You will be prompted to select the sequence element that you would like to begin at the origin.
- Beta version workaround: convert the circular construct to a linear construct, rearrange the elements so that the desired element is at the left end and convert back to circular.
Viewing the backtranslation profile
- Backtranslation in GeneDesigner uses a genetic algorithm to avoid getting stuck in suboptimal local minima.
- Backtranslation profiles can be created and edited from the “Configure” pull down menu at the top of the Construct Editor
- The backtranslation profile allows you to control
- The genetic algorithm
- The codon bias table and threshold
- Unwanted sequences that will be excluded from backtranslated sequences, including
- restriction sites
- cryptic splice sites
- ribosome binding sites
- The size of repeats that the software attempts to eliminate.
- By storing backtranslation profiles you can use the same parameters for many constructs without having to re-enter the same data every time.
- More details on backtranslation can be found here
Profile differences
- The Details View will indicate whether there are differences between the profile applied to a construct, and a profile that may have the same name in the profile manager.
- This is intended to avoid confusion when
- Two people share a construct and may have different backtranslation profiles with the same name
- A backtranslation profile has been edited, but the new values apply only to that construct.
