Part C: Running the script

This part of the tutorial will demonstrate several ways to run a SeqNinja script. When you “run” a script, you tell SeqNinja to execute all of the steps in order from top to bottom. The results are then output into the data file and format that you specified in the script.

There are several ways to initiate a run.

• Choosing Run > Run from the menu or clicking the Run tool () initiates a run without allowing you to choose any options.

• Selecting Run > Run with Options instead launches the following dialog. This dialog allows you to override some of the global preferences from the Edit > Preferences dialogs, but for this script only. A useful feature in the Run with Options dialog is the Overwrite existing files without asking checkbox. You may check or uncheck this box to hide/show warnings about over-writing an existing data file.

1. For this tutorial, simply press the Run tool (). Alternatively, if you opened the Run with Options dialog, keep the settings shown in the image above and click the Run button. When the run is complete, the Run Completed dialog is displayed:

If the run was successful, there will be a single tab, called Files. The Files tab contains a table listing the names of any output files, with links to their directories.

*Note: A second tab, entitled Warnings, may appear after some runs. This tab provides additional information about the run, including warnings about errors (e.g., syntax errors) or about the possibility of unexpected results. For example, if you attempt to reverse complement a protein, the Warnings tab will advise you that the sequence being reverse complemented appears to be a protein.

2. In the Files tab of the pop-up window, click the link to go to the tutorial data folder.

3. Open the output file pBR322-amended.gb in DNASTAR’s SeqBuilder Pro application or in any text editor. Note that the three ‘A’ bases appear, as specified, between base 24 and the base that was formerly base 25.

4. Close SeqBuilder Pro or the text editor and return to SeqNinja.

This is the end of Tutorial 1.