IMC i05 Fragment Assembly on PlasmidMap

This is an overview of Fragment Assembly on PlasmidMap, a feature derived from the DNA Fragment Assembly Workbench, whose full scope was released in Version 9.3.

Fragment Assembly on PlasmidMap is a tool for ligating multiple DNA fragments, including vectors, in any order. The feature is divided into the following steps.

• A. The selected GenBank-format DNA fragment files (vectors can be included) in the current folder of the IMC Main Directory Tree are provisionally joined in the order shown in the tree (simply arranged without actually performing ligation), and drawn as either a circular or a linear plasmid map.
  • A-1. All Feature Keys annotated on each DNA fragment file can be displayed.
  • A-2. The display attributes that can currently be edited for each Feature Key are as follows:
    • Show/hide selection for each Feature Key
    • Feature Key drawing color
    • Order of the concentric circles in which it is displayed
    • The Feature Key qualifier used to identify each feature
    • The shape used to display features (currently a choice of 3 types)
• B. The PlasmidMap features are as follows:
  • B-1. The Radial zoom function enlarges/shrinks the circular plasmid map in the radial direction.
  • B-2. It has a linear sequence lane, which displays the base sequence of the currently selected sector as a double strand.
  • B-3. The Radial handle for specifying a sector lets you drag around the circular map to specify the region displayed in the sequence lane.
  • B-4. There is a jump function to move directly to a provisional junction.
• C. A primer design function for joining DNA fragments at a provisional junction region is implemented.
  • C-1. The Assembly methods currently implemented are as follows:
    • Gibson Assembly
    • In-Fusion Assembly
    • Golden Gate Assembly
    • Seamless Ligation Cloning Extract (SLiCE)
    • Yeast Homologous Recombination
    • USER Cloning / USER Assembly
    • Overlap Extension PCR
    • MoClo / Golden Braid / BASIC
  • C-2. You can select a candidate primer sequence by dragging the mouse near a junction region on the sequence lane.
  • C-3. Any restriction enzyme recognition site can be added to the selected candidate primer sequence.
    • Editing of the recognition site is locked.
  • C-4. The selected candidate primer sequence can be edited.
  • C-5. The Tm, GC content, and other properties of the selected candidate primer sequence are calculated.
• D. The designed candidate primer sequences are saved as primer data under any file name.
  • D-1. Any prefix can be attached, with a sequential number starting from any value.
  • D-2. The DNA fragment sequence information referenced during the design can also be saved.