Defining and Editing Gene and Domain Definitions
In this example we will demonstrate how to specify coding and non-coding regions of a sequence. We will be using the file “Contigs.meg” which is located in the MEGA/Examples directory folder (The default location for Windows users is C:\Users\UserName\Documents\MEGA7\Examples\. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the user’s home directory).
Example 6.1:
Activate the data file "Contigs.meg". If necessary, refer to Example 1.2 of the “MEGA Basics” tutorial.
From the main MEGA window launch bar, select Data | Select Genes and Domains.
Notice the column header bar across the top (‘Name’, ‘From’, ‘To’, ‘#Sites’, ‘Coding?’ 'Codon Start’). Domains will be listed under the column header labeled ‘Name’. Click on the domain labeled Data underneath the Genes/Domains group, then click on the button labeled Delete/Edit. Select Delete Gene/Domain to delete the data domain.
Click on the Genes/Domains label and then click the Add Domain button. Select Add New Domain from the popup menu.
Right-click on the new domain and select Edit Name from the popup menu. Change the name to “Exon1” and press the Enter key.
Select the ellipses (…) button next to the first question mark in the ‘From’ column to set the first site of the domain. When the Start site for Exon1 window appears, select site number 1 for the AC087512 chimp row and push the Ok button.
Select the ellipsis (…) button in the ‘To’ column to set the last site of the domain. When the End site for Exon1 window appears, select site number 3918 for the AC087512 chimp row and push the OK button.
Check the box in the ‘Coding?’ column to indicate that this domain is protein coding. You will need to click the box three times before the check mark appears.
Add two more domains to the Genes/Domains item using the same steps. One of these domains will be named “Intron1” and will begin at site 3919 and end at site 5191. The other will be named “Exon2” and will begin at site 5192 and end at site 8421. Be sure to check the checkbox in the ‘Coding?’ column for Exon2 to indicate a protein-coding domain.
Click on the Genes/Domains item to highlight it and then click the Add Gene button at the bottom of the screen. From the popup menu choose Add new gene at the end. Right click on this new gene and change the name to “Predicted Gene”. Click and drag all of the newly created domains to the Predicted Gene so that they now appear under the new gene.
Press the Close button at the bottom of the window to exit the Gene/Domain Organization window.
Using Domain Definitions to Compute Pairwise Distances
Now, if we compute pairwise distances between our sequences, the non-coding regions that we specified in the example above will be ignored.
Example 6.2:
From the main MEGA window, select the Distance | Compute Pairwise Distances option from the launch bar.
In the Analysis Preferences window, click on the Substitutions Type drop-down and select Nucleotide. The Select Codon Positions row is now enabled. Make sure that the Noncoding sites option does not have a checkmark next to it. Click the Compute button to begin the analysis.
When the computation is complete, the Pairwise Distances window will display the pairwise distance computed using only the sequence data from exonic domains of the Predicted Gene. Close the Pairwise Distances window by selecting File | Quit Viewer and the Sequence Data Explorer window by selecting the Close Data icon on the main MEGA window.