Tutorial: Running Summary Analyses

Gene Inspector allows you to run Summary Analyses on multiple sequences at once and it will present the results in a single output object. From within the resulting output object it is possible to see explore details of any of the individual sequence analyses it contains. Summary Analyses are described in this tutorial. Summary Analyses are available only for appropriate analyses.

  1. Choose AnalysesNew Analysis and then choose to do a Protein Analysis; finally select the “Find Sequence” analysis and press OK.
  2. You will see a dialog like that shown in Figure 19. Notice that there is a “Show Summary Results” checkbox circled in the figure. You should click in this box to turn it on. Type aaaa into the Sequence field as the sequence to search for and then click on the <empty segment 1> text in the list box above to enter that sequence. For the number of allowable mismatches, enter a 1. There is no need to enter anything in the other fields.
    Figure 19: Find Sequence Dialog

  3. Now click on the Input Sequences icon to choose the sequences you will be using in this analysis. For this analysis you will examine all of the acetylcholine receptors. You should see something resembling Figure 20. Click the Add… button to bring up the sequence chooser dialog.
    Figure 20: Input Sequence Dialog

  4. After pressing the add button you will see the dialog box shown in Figure 21. This allows you to choose which sequences will be analyzed. Find the Peptide Sequences folder in your GI sequences folder and click once on the file acetylcholine recpts. This will place the names of all the sequences in this file into the list in the lower left of the dialog box. Now press the Add `acetylcholine recpts’ >> button to add this file (containing the 9 sequences) to the Chosen files and sequences list in the lower right of this window. After adding these sequences, press the Done button to return to the analysis setup panel.
    Figure 21: Choosing Sequences for Summary Analysis

  5. Press Run to run the analyses.
  6. You will see the summary result object appear in the notebook as shown in Figure 22. This object lists the 9 sequences examined, the number of matches found within each of them, and indicates on a linear map where the matches exist. This object is a summary of the search results for the query sequence. It provides you with a graphic overview of the matches found and serves as a starting point for further analysis. Without using the Summary Analysis option in the setup panel, the results would have been displayed as nine separate Find Sequence analyses.
    Figure 22: Summary Result Output Object

  7. Double-click on the output object to target it and then click on the Chick musc Ach Recpt item. Now choose the Object Search Selected Sequences… menu item to launch the detailed (single sequence) analysis on the chosen sequence. You will see the analysis setup panel open with all appropriate parameters already filled in for you. Press Run to conduct the analysis. The results will be seen as a new object in the notebook as shown in Figure 23.
    Figure 23: Find Sequence analysis

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.

This entry was posted in gene inspector tutorials and tagged , , , , , . Bookmark the permalink. Post a comment or leave a trackback: Trackback URL.

Post a Comment

Your email is never published nor shared. Required fields are marked *


You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>