Tutorial: Using Analysis Setups

This tutorial focuses on running analyses. Together with Tutorial 1: Tour of a Gene Inspector Notebook and Tutorial 2: Editing Sequences this tutorial provides an overview of the three main parts of the Gene Inspector.

  1. Analysis Setups are a key concept in the Gene Inspector. They are how you initiate an analysis and they provide a way for you to create and later return to a specific analysis or set of analyses. Choose Analysis New Analysis…. This will bring up the Analysis Chooser shown in Figure 7. At this point you could choose to do either a protein or nucleic acid analysis. For this tutorial press the radio button at the top of the dialog to specify that you will be doing a Protein Analysis. The text area on the right of this window always provides information about the analysis that is selected in the list on the left side of the window, in this case Transmembrane Helices. Also, note that the list can be displayed as a text list or as an icon list shown here by using the draw icons check box.
    Figure 7: The Analysis Chooser

  2. Select Transmembrane Helices from the list on the left and press the OK button. This will create a new Analysis Setup. Analysis Setups contain a number of different panels, each represented by an icon on the left of the window. The Analysis Setup panel for Transmembrane Helices is shown in Figure 8.
    Figure 8: The Analysis Setup Panel

  3. Notice the popup menus on the right of the Analysis Setup Panel. The Table popup menu offers choices for the tables of values to be used in the analysis calculations. Choose the Argos, et al. table. The Style popup menu allows you to set a style for the output. We will talk about style sheets later; for now leave it at the default value.
  4. Click on Input Sequences on the left of the Analysis Setup Window, and press the Add… button (Figure 9). This will bring up the sequence chooser window shown in Figure 10. Find the “Peptide Sequences” folder which is inside the GI Seqs folder and click on the “rhodopsins” file. This file contains a number of rhodopsin sequences, which will appear in the bottom left list as soon as you click on the file in the top left list. Note that the list on the top left is a list of files, similar to what you see in other applications when you choose to open a file.
    Figure 9: The Input Sequence Panel

    However, because the Gene Inspector allows you to store multiple sequences in a single file, you need to specify not only the name of the file, but the name of the sequence(s) within the file with which you wish to work. This is the reason for having the more detailed dialog box shown here. If you press the Add `rhodopsins’ >> button (or double-click the file name in the top left list), the entire file will be added to the Chosen files and sequences list in the bottom right. For this tutorial, just double-click on the octopus rhodopsin sequence in the bottom left. Octopus rhodopsin will appear in the bottom right list of Chosen files and sequences . One or more sequences can be chosen from one or more sequence files. The analysis will be performed on every sequence in this list on the right. Also choose Lamprey rhodopsin and add it to the Chosen files and sequences list on the right. Press the Done button to indicate that you have no more sequences to be analyzed.

    Figure 10: The Sequence Chooser

  5. Finally, you need to specify a location for the output from the analysis. This is done using the Output Location panel which can be selected from the icon list on the left and is shown in Figure 11. Using the popup menu in this panel, you can specify that the output generated will be placed in a new notebook, or added to any currently open notebook (all of which are listed in the popup menu).
    Figure 11: Output Location Panel

  6. Before you run the analyses, note that at the top of the Analysis Setup you have selected two sequences (inputs) and one analysis – therefore, you will have two output objects. The information at the top of the window always lets you know how many output objects you will be generating. The High Priority option is discussed elsewhere – leave it unchecked for now.
  7. To start the analysis running and close the Analysis Setup Window, choose the Run button (the Close button would just close the panel without starting the analysis).
  8. Once the analyses have been launched, they will appear in the Analysis Monitor. You can see the analysis monitor by choosing Analysis Show Analysis Monitor. The Analysis Monitor shows the status of each analysis being run and will also show the order in which analyses are to be run. The Analysis Monitor will indicate the progress of each analysis as it is run. Most analyses will run so quickly that unless you already have the Analysis Monitor open when the analysis starts, you will not be able to see the analysis listed in the Analysis Monitor because it will be done before the window opens.
  9. Each completed analysis becomes an object in the GI Notebook. Click once on an output object to make it the selection and note the appearance of 8 black square dots (called “handles“) along the edges of the object. The selected object can be moved around on the page by dragging with the mouse. The handles can be used to resize the object by clicking and dragging one of the handles with the mouse. This is similar to the way objects behave in many drawing programs.
  10. Save the notebook in a location on your hard disk that you will remember by choosing File Save As… and give it a name you will remember. You will need the notebook to continue with the tutorial Tutorial 7: Aligning Analysis Objects.

This concludes this tutorial. You may quit or continue on to the next tutorial.

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