====== Cloning Tool ======
The //in silico// cloning tool allows you to computationally create restriction fragments and assemble them by ligation.
  * It is accessed from the "Tools" menu in the [[ui:Construct Editor]]
   

===== Creating Fragments =====
(link to screenshot 13)
==== Importing the fragment donor ====
Restriction fragments can be created by dragging 
  * Any vector, construct, element or group of elements from the [[ui:library_explorer | Library]]
  * Any construct, sequence element or group of elements from the [[ui:navigation_pane | Navigation Pane]]
  * Any construct, sequence element or group of elements from the [[ui:workspace_pane | Workspace Pane]]
into the Input Pane (label in screenshot 13)

==== "Cutting" the DNA ====
=== Choosing restriction sites ===
DNA is digested //in silico// by choosing one or more restriction sites from the Sites Pane (label in screenshot 13)
  * Restriction sites can be selected from all possible sites by
    * typing in the beginning of the restriction enzyme name in the box at the top of the "search all" tab
    * clicking on the sites of interest
  * Restriction sites can be selected from one of your lists of [[guide: managed lists]] of sites by
    * selecting the "my sites" tab
    * selecting the list name from the pull down menu
    * clicking on the sites of interest
  * Once the sites of interest have been selected, click on the "choose" button at the bottom of the Sites Pane (label in screenshot 13)

=== Cutting a fragment ===
  * Once one or more restriction sites have been chosen, the sites will be shown
    * marked as lines on the graphical map in the Input Pane (label in screenshot 13)
    * as site names and positions in the Digestion Pane (label in screenshot 13)
      * when the mouse hovers over a site on the map in the Input Pane, it is highlighted in the Digestion Pane, and //vice versa//.
  * A fragment can be cut by selecting the restriction sites that flank it, either by
    * clicking on the site in the graphical map, or
    * clicking on the site in the Digestion Pane
  * "Cutting" the DNA will cause a segment of DNA to drop out of the fragment donor
    * Any "cut" segments of DNA may be dragged from the Input Pane to the Ligation Pane (label in screenshot 13) for assembly into the final construct.

===== Ligating Fragments =====
(link to screenshot 13)
=== Fragment display ===
  * "Cut" fragments of DNA that have been dragged from the Input Pane to the Ligation Pane (label in screenshot 13) are displayed
    * with their 5' and 3' overhangs shown
    * elements within the fragments can be seen by hovering the mouse over each element: the element will be highlighted in the [[ui:Navigation Pane]] 
  * Each fragment becomes a single group, named after its construct and location of origin.
    * The fragment also retains all of its internal structure of groups and elements

=== Rearranging fragment order ===
  * Fragments can be rearranged by dragging them up or down in the Ligation Pane
    * Prior to the ligation step, the right overhang of each fragment must match the left overhang of the following fragment.

=== Cloning ===
  * Once the fragment overhangs all match each other, press the "Clone" button at the bottom of the Ligation Pane
    * The resultant construct can be dragged into the Design Toolbox or Vector Library in the [[ui:library_explorer | Library]], or as a new construct in the [[ui:navigation_pane | Navigation Pane]] of the [[ui:Construct Editor]]