The "Product" tab pane and "Matrix" tab pane are located at the bottom of the left pane of the WB:DNA Assembly Workbench. This section describes the operations in the Product tab pane.
There are many buttons, which are classified into the following four types:
- A group of buttons for running ligation simulation and execution
- Product table selection operations
- Product filter-out functions
- Product save operations
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Group of buttons for running ligation simulation and execution
- Simulate Ligation button: With two or more fragments selected in the Fragment Table, clicking the Simulate Ligation button runs a ligation simulation. This does not perform actual ligation; it only shows the possibility. At this point, fragments with ligation possibility are arranged on the Ligation Canvas on the right, in the order in which they could be joined, with the overhangs to be joined shown in colored bases and aligned. However, if a product could become circular, it is not actually circularized; instead it is shown as linear DNA starting from the fragment with the lowest fragment ID, and a circular icon is shown at the head of that product. At the same time, the product table shows a list of candidate products made up of combinations of fragments with ligation possibility.
- Ligate button: After running Simulate Ligation, clicking this button joins the fragments together to generate a single product sequence. The Ligation Canvas in the right pane shows a preview image with the overhangs actually joined.
Display of expected simulation numbers (shows the expected results of the ligation possibility simulation):
- Total (N1): The expected number of products
- Full Chain (N2): Of those, the number of products that use every fragment exactly once
- Drawn (N3): The number of products drawn on the Ligation Canvas
Product table columns:
- Check box: Selects the products to operate on.
- Ligated: After ligation is executed, products that were actually ligated are checked automatically.
- Product ID: An ID automatically assigned in display order, with the prefix "P" followed by a sequential number starting from 1.
- Total Length: Shows the base length of the product. For products that circularize, a value that double-counts the overhang region is shown in parentheses.
- 5'End Preview: A double-strand base display and phosphorylation display of the product's 5' end
- 3'End Preview: A double-strand base display and phosphorylation display of the product's 3' end
- Preview: Shows the base composition of the product's ends and junctions, color-coded by base.
Product table selection operations
Products in the product table are selected by turning the checkbox on or off. In addition, the Select All button selects all products, and the Reverse Selected button reverses the current selection state.
Product filter-out functions
This function filters out unneeded products when a large number of products is expected to be generated.
- Show All: When this is on, no filtering is applied, and all products with ligation possibility are shown.
- Full Chain Only: Products other than those that join all of the selected fragments are filtered out.
- Fragment count range (n ~ m): Products whose fragment count is outside the specified range are filtered out.
- Circular products only: Products other than those that become circular are filtered out.
- Group Duplicate Circular Structures: When multiple circularizing products share the same structure, all but one of them are filtered out. The one that is not filtered out is the product in which the fragment with the lowest fragment ID comes first.
Product save operations
Products in the product table for which ligation has been executed, and which are checked, are saved as GenBank files to a specified directory.
The save directory is specified in the directory selection dialog that appears when you click the Choose Directory... button.
Saved files can use either of the following naming methods:
- Use the automatically generated product ID as the file name.
- Save with a file name consisting of a specified prefix followed by a sequential number starting from a specified value.