3.3.6 Restriction Analysis

Details about this feature can be found in the main Genome Compiler user guide:

See section 1.17 for Managing Restriction Sites.

See section 1.18 for Virtual Digest.

  • In ApE, after opening a molecule you should open the “Enzyme Selection Dialog” to select the appropriate enzymes and then open the “Digestion window” to view the results. The “Enzyme Selection Dialog” can be launched through the main tool bar (Figure 3.3.6.1) or from the main menu by choosing “Enzymes”-”Enzyme Selector” (Figure 3.3.6.2). In order to open the “Digestion window” go to “Enzymes”-”Digestion” from the main menu (Figure 3.3.6.2) or choose the icon from the main tool bar (Figure 3.3.6.1). To highlight the selected enzymes in the sequence/graphical windows you should press the icon from the main tool bar (Figure 3.3.6.1) or go to “Enzymes”-”Highlight” from the main menu (Figure 3.3.6.2).

    Figure 3.3.6.1: Restriction Analysis icons in the main tool bar in ApE.

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    Figure 3.3.6.2: Restriction Analysis tools in the main menu in ApE.

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  • In Genome Compiler you can manage restriction enzymes through “Restriction Sites” dialog (Figure 3.3.6.3). You can filter them for different criteria and save presets for further use. To open the “Restriction Sites” dialog, right click on the restriction enzyme in any of the views (Linear/Circular/Sequence) and select the “Restriction settings” from the drop down menu (Figure 3.3.6.4). For more information on managing restriction sites please refer to section 1.17.

    Figure 3.3.6.3: “Restriction Sites” dialog in Genome Compiler.

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    Figure 3.3.6.4: Opening the “Restriction Sites” dialog through right click-“Restriction settings”.

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  • In Genome Compiler in order to perform a hypothetical digest on a sequence selection or on the whole project you should open the “Run Digest” dialog (Figure 3.3.6.5). This dialog can be opened by clicking on “Digest” in the main tool bar (Figure 3.3.6.6) or through opening the “Tools” drop down menu and choosing “Digest” (Figure 3.3.6.7). Alternatively you can right click on project canvas or the project tab and select “Run Digest” (Figure 3.3.6.8). For more information on handling the “Run Digest” dialog please refer to section 1.18.

    Figure 3.3.6.5: “Run Digest” dialog in Genome Compiler.

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    Figure 3.3.6.6: Opening the “Run Digest” dialog through “Digest” in the main tool bar.

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    Figure 3.3.6.7: Opening the “Run Digest” dialog through Tools-Digest.

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    Figure 3.3.6.8: Opening the “Run Digest” dialog through right click-“Run Digest”.

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