What is a Quagga?

Making a Sequence Alignment

A sequence alignment is a way of organising related sequences so that the differences among them show evolutionary change.
Here you will import the sequences obtained by the Wilson group into a desktop program called Geneious to complete the alignment and subsequent phylogenetic analysis. Geneious is a popular program for managing and analyzing DNA sequences.

Get Geneious

Take a few minutes now to download and install Geneious, and become familiar with navigating in the program. Return to this window when you are ready to proceed with the Quagga story. [Get Geneious]

Get the sequences

If you have already downloaded the sequence file, then skip ahead.
You will need the file of DNA sequences obtained the Wilson group.   Whatisaquagga (1 KB)  Right-click on the sequence image, choose Save the Link As ... and save the file on your desktop computer.(Please extract zip file before use) .

Import the Quagga Sequences

The sequences obtained by the Wilson group need to be imported into Geneious.

Make a working folder to store your analysis.

• In Geneious, click on the Local folder in the left-hand Sources window.
• In the File menu, choose New folder to make a new folder.
• Give the folder a name.

Import the sequences.

• Select your new folder.
• In the File menu, choose Import ... From File ...
• Select Auto-detect format and click OK.
• Browse to find your file.

The sequences will now be listed. You can view them individually by clicking on each in turn.
As you scan through them, notice that the sequences for the nd1 and co1 regions are inter-mixed.

Align the sequences

You need to construct two sequence alignments, one for each of nd1 and co1.

• In the list of sequences, select all five sequences for one of the genes.
  • Click on one sequence and then control-click (Windows) or command-click (Mac) on the others.
• Construct the alignment.
  • Click the Alignment tool.
  • In the dialog box, click OK to accept the standard method.
• Repeat this process for the other gene region.
• You will now have two sequence alignments, one for each gene.

 

Return to the Research Plan for the next step.