Working With Genes and Domains
Ex 5.0.1: Start MEGA by double-clicking
on the MEGA desktop icon, or by using the Windows start-menu to click on the
MEGA icon located in the programs folder.
Ex 5.0.2: Activate the data present in
the Contigs.meg file by using the File|Open command.
We will now examine how to define and edit gene and
domain definitions
Ex 5.1.1: Select the Data|Setup|Select Genes & Domains menu command.
Ex 5.1.2: Delete the Data domain by
right clicking on it and selecting Delete
Gene/Domain from the popup menu.
Ex 5.1.3: Right-click on the
Genes/Domains item in the Names column, and select Add New Domain. Right-click on the new domain and
select Edit Name from the popup menu and set the name to “Exon1.”
Ex 5.1.4: Select the ellipsis button
next to the question mark in the From column to
set the first site of the domain. When the site selection window appears,
select site number 1 and push the “OK” button.
Ex 5.1.5: Select the ellipsis button in
the To column to set the last site of the
domain. When the site selection window appears, select site number 3918 and
push the “OK” button.
Ex 5.1.6: Check the box in the Coding
column to indicate that this domain is protein coding.
Ex 5.1.7: Add two more domains to the
Genes/Domains item. 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.
Ex 5.1.8: Right-click on the
Genes/Domains item and select Insert New Gene from the popup menu. Change the
name of this gene to “Predicted Gene,” and click-and-drag all of the domains to
this new gene such that they are displayed as children of the “Predicted Gene”
node in the display tree.
Ex 5.1.9: Press the “Close” button at
the bottom of the window to exit the Gene/Domain manager.
We will now use these domain definitions in computing pairwise distances.
Ex 5.2.1: Select the Distances|Compute
Pairwise menu item from the main menu.
Ex 5.2.2: On the Include Sites
tab, make sure that the “Noncoding sites” option
does not have a checkmark next to it. Go back to the main menu and press the
“Compute” button to begin the analysis.
Ex 5.2.3: When the computation is
complete the Distance Explorer will display the pairwise
distance computed using only the sequence data from exonic
domains of the “Predicted Gene.”
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