Now that you have completed Part B, step 2, you will automatically locate and add features to the consensus using a BLAST search.

  1. In the Project Summary window, select Contig 5 (if it is not already selected).
  1. Select Net Search > Blast Selection. Keep all settings at the defaults, and then press OK.

Wait for the results window to be populated. This will take approximately 3-5 minutes.

  1. By default, the rows are sorted first by organism, and then by score. To select the top-scoring BLAST result based solely on the score, click once or twice on the Score column header until the scores appear in descending order.

The first row is a 100.0% match for Contig 5 over a specific region — in this case, the entire contig (100%). To copy the features from the top match to the consensus, click on the first row to select it, and then choose Collect Features.

  1. Leave the Save dialog settings at their defaults and click OK.

The Feature Table will open automatically. The table shows the type, name and location of each imported feature.

  1. To view the features in the Strategy View, choose Contig > Strategy View.
  1. In the Strategy View’s Features from drop-down menu, choose Consensus.

  1. Depending on the size of your Strategy View window, at least some features should now be visible as thick arrows to the right of the drop-down menu. To see all of the features, do one of the following:

    • Use the scrollbar to the right of the features to scroll down.



    • Maximize the Strategy View, and then drag the horizontal pane divider (thin double line) downward with the mouse.

      Depending on the size of your screen and the number of features, this procedure may allow you to see most or all of the features simultaneously.

  1. Hover the mouse over any feature to view an information balloon.

  1. Click on any feature to select it, and then double-click on it to open a two-tabbed Feature Editor. The editor is used to view and/or edit information such as the feature title, location, and description.

The default tab is the Location tab:

Click on Description to reveal a second dialog of editable feature information.

  1. Close the Feature Editor by clicking Cancel, then close the Strategy View. Be sure to leave the Feature Table open.
  1. Returning to the Feature Table, experiment with the following:

    • To show or hide columns - Right-click and choose Show/Hide Column, then check or uncheck boxes.

    • To move a column - Use the mouse to drag and drop it in the desired location.

    • To sort data in alphabetical or numerical order - Click on the column header that you wish to sort.

    • To hide one or more features - Click the associated checkmark(s) in the Visible column. Then, return to the Strategy View to verify that the feature is no longer being displayed.
  1. When you are done, individually close all the windows except the Project Summary window.

Proceed to 4. Ordering contigs into scaffolds.

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