Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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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.”