This describes the features of the DNA Fragment Assembly Workbench, whose full feature set was released in Version 9.3. The DNA Fragment Assembly Workbench is broadly divided into the following functions.
- A Runs a ligation simulation on all fragments in the current folder selected in the MainTree.
- A-1 The end shape of each fragment in the fragment table is shown graphically.
- A-2 The phosphorylation (-PPP) / dephosphorylation (-OH) state of each fragment and product is shown graphically.
- A-3 You can specify filters to narrow down the ligation products.
- A filter to show only products that become circular
- A filter to show only products consisting of at least a specified number of fragments
- A-4 You can draw a plasmid map, in the order shown in the fragment table, for all fragments selected in the fragment table, without actually ligating them.
- A-5 If the number of products that would be generated exceeds a specified value, execution is suppressed. The default is 1,000,000.
- B Graphically displays combinations of fragments that could potentially be ligated.
- B-1 Fragment ends that can be ligated are shown side by side, with overhang bases shown in color, making it easy to see ligation possibilities.
- B-2 Products that would become circular DNA are marked with a circle icon, making it easy to see whether circularization will occur.
- B-3 Each fragment is shown in a different color, making it easy to identify fragments.
- B-4 Products drawn on the ligation canvas can be zoomed in two dimensions. Right-click and drag the mouse along X/Y to zoom according to the X/Y ratio.
- B-5 After reviewing the ligation simulation results, if they look correct, click the "Ligate" button to actually execute the ligation and generate the needed product.
- C Displays a table of ligation products.
- C-1 The order of fragment IDs is shown in the product table.
- C-2 The end shape of each product is shown graphically in the product table.
- C-3 The phosphorylation (-PPP) / dephosphorylation (-OH) state of each product is shown graphically.
- C-4 The total base length of the product, before and after circularization, is shown. The value in parentheses is the length before circularization.
- C-5 The junction points between fragments, their end states, and whether circularization occurred are shown in the Preview column.
- C-6 Ligated products can be simulated on a gel electrophoresis with any restriction enzyme.
- D Saves the ligation product as a GenBank-format file in a specified folder.
- D-1 The saved GenBank file name can be specified using a given prefix together with a sequential number starting from a given value.
- E In addition to the "ligation simulation and execution" functions in A–D, there is also a way to extend the ligation product by dropping selected fragments one at a time onto the Construction Canvas.
(This feature is currently under development, but some of it can already be used.)- E-1 Fragments (including vectors) can be dropped one at a time to build up the construct while extending the ligation product.
- E-2 Dropped fragments can be removed from the canvas.
- E-3 A plasmid map of the resulting product can be drawn.
- E-4 As with the ligation products in C, it can be saved as a GenBank file.