Contents of this Article
Assembly Reports
TeselaGen's software has the potential to create Assembly Reports from your designs using the J5 DNA Assembly Design Automation Software. Each report will include a series of sections including assembled constructs, oligos, PCRs, assembly pieces, etc. Your reports are stored in a library, which you can access from the Molecular Biology Toolkit on the left side panel.
Reports allow you to gain insights into your designs. This analysis breaks down your design and gives you the input pieces, oligos, and PCR reactions needed to assemble it in a lab. It is based on a cost-benefit analysis and the pieces and restrictions you set on your input design.
Adding a New Report
To create a new report from a DNA design, locate the "Submit for Assembly" option on the upper right corner when working on a design.
Once your report is created, you can see its status and details on the DNA Assembly Reports library.
Warnings
Notice in the image below that some entries are completed, and others (yellow dot on the status column) have warnings that need to be checked.
Warnings can have several statuses: a report can be completed (green) or have warnings (yellow). To see the warnings, open the report and locate the first section: Assembled Constructs. Notice that you need to open the construct to see them in detail.
When opening the construct, you can locate the warnings on either the plasmid or sequence map view, they appear in yellow (if you can't see them, make sure the view is enabled on View > Warnings). They indicate that the Assembly Report found something in your design that may cause you trouble when working.
In the example above, the warning (on the plasmid view) shows a homologous sequence repeat. By placing the cursor over it, you can see a brief description (which you can also open on a pop-up window by double-clicking on the warning). On the sequence map view, you can also see the warnings on a similar display as an annotation.
A yellow warning can be edited, or you can use the contents of your assembly report without making any changes to your design. However, when the status of the report is "Error" (red), you will notice that the analysis does not create any constructs, and you need to click on the "View Warnings" button on the information about the report.
This will open a pop-up window with the information about the warning. To be able to submit your design for an assembly analysis, you need to fix the error shown.
Next, let's examine the contents of a DNA Assembly report in detail.
Contents of a DNA Assembly Report
A typical DNA Assembly Report includes 10 sections. To examine the contents of each one of them, let's take as an example the Combinatorial Golden Gate DNA Assembly we created on a previous tutorial:
The sections found in the report are:
Assembled constructs: Gives you the possible options for your final construct. The example design is combinatorial (some DNA sequences have more than one part to choose from) so the Report generated eight possible assembled constructs. When opening them, notice that primers are included in the annotations of the sequences.
Input sequences: Shows a list of the sequences used in your design (represented by bins on the design view).
Input parts: Shows a list of the DNA parts used. This number may differ from the Input sequences if you have a combinatorial design. In the example used, we have 5 bins, but in total, we used 9 different DNA Parts.
Assembly oligos: they need to be synthesized
Annealed oligos
Digest Linearized Fragments: fragments that are going to be used on the assembly reaction
Synthon sequences: List of DNA pieces that need to be directly synthesized
PCRs; PCR reactions that need to be run to generate the assembly pieces
embed in sequencing vector?
Assembly pieces: Pieces of DNA that will get put together in a final assembly reaction to give the desired constructs
Assemblies: lists which assembly pieces need to be combined to create each construct