Tutorial
Select Add -> Add part from the top right menu:
This will open an 'Add new part' form in the main area of the designer.
Fill in the required information:
- Part name: Type in a name of a new part.
- GenBank file: click to select a file, containing the sequence of a new part. Note that it should have no overhangs or flanking restriction sites. They will be added automatically. Alternatively use Sequence field to enter the sequence manually.
- Baseseq: Select one of the Base sequences. This will determine a plasmid for the new part. Most probably you want to select 'L0'. See more info about BaseSeqs on the Tables page and in Setting up a schema section.
- Backbone: Select one of the Backbones. This will determine the adapter overhangs to use for the new part.
Click on the Save button in the bottom of the form. If no errors appear, you will be able to find your new part in the corresponding folder in the navigation panel:
Click on the part to view its sequence and a plasmid map. Use action buttons above the plasmid map to edit the name of the part, download the complete sequence of the plasmid or delete it:
You can alternatively add multiple parts, stored in a multi-line FASTA file. Note that, as in case with one part, the sequences should be bare, i.e. contain no sequences of the plasmid, restriction enzyme sites or overhangs.
Select Add -> Add multiple parts from the top right menu:
Click inside FASTA file field and select the file you want to upload.
Click on the Upload button in the bottom of the form. This should generate a new form with one row per each sequence in the selected FASTA file:
Select the Baseseq and Backbone for each of the parts and click on the Save button in the bottom of the form. This should add your parts to the corresponding folder in the navigation panel.
Select Add -> Assemble part from the top right menu:
This will open an 'Assemble new part' form in the main area of the designer.
Start by selecting the Backbone you want to use for the assembly.
You will be then asked to select the first part for the assembly. On this and consecutive steps the choice of parts will be limited to those, having a 5' adapter overhang matching the 3' adapter overhang of the previous part, or the 5' receiver overhang of the selected backbone for the first part. If you have a part in your collection, but it is not it the list, check that it has the right backbone assigned and that you are selecting it at the right step of the assembly.
The assembly automatically finishes, when the 3' adapter overhang of the selected part matches the 3' receiver overhang of the plasmid. At this point you will be asked to enter a name for the new part and save it by clicking Finalise.
If you select a part, which doesn't have a matching overhang you will be presented with an 'Can't find parts to proceed assembly.' message. You can go backward stepwise by clicking the Back button in the bottom of the form.
When you select a part with a level higher that zero from you collection, you will see a protocol table below the sequence panel. The number of columns correspond to the number of children parts, that make up the part you've selected. The three rows contain information about the names of the backbone and all the children, the lengths of the complete plasmids and concentration they should be diluted to in order to use them in the standard Loop Assembly protocol (using 1 uL of each of the children parts and 1 uL of the backbone).
We suggest to copy tables of all the parts you want to assemble in one big table, print it out and take to the bench, where it will guide you during the assembly.