The aim of this exercise is to understand and generate multiple alignments.


1. Download the program Se-Al from the course website. This is a sequence editing program used to alter multiple sequence alignments.

2. Use ClustalW to align the DNA sequences from the ZP3 gene on the website. This is the coding region for the ZP3 gene. The sequences are in fasta format. Request that the output be given as "pir" format. Save the alignment as a text file onto the desktop.

3. Open the alignment from above in the Se-Al program. Check the alignment by eye. Do you see any errors? For coding sequence, gaps should occur in frame. Change the alignment view to codons (under "alignment" menu, select "alignment type" then "codons"). Do you see any errors? Now view the alignment as amino acid. Do you see any errors?

4. Download the ZP3 aligned protein sequence. Use this alignment to guide the alignment of the ZP3 DNA sequences using Protal2DNA (link on website). Select the output to be in Pearson/Fasta. Save the aligned DNA sequence to the desktop and open the file in Se-Al. How does the alignment look? Are the gaps in frame? Do you need to do any sequence editing?
a. This program is very picky. If you want to use it on your own data, you will have to edit the Clustal protein alignment to look like the file I am supplying. The order of the sequences must be the same in the aligned protein sequence and nucleotide unaligned nucleotide sequence.

5. Choose a sequence of your own interest and perform a multiple sequence alignment. If using protein coding sequence, you may want to use Protal2DNA. If you are using non-coding sequence just use Clustal. View the alignment in Se-Al and edit the alignment by eye. Describe any errors. Provide a print out of the first page of your alignment. Save this alignment for future labs.

6. Write up a 1 page description of what you did in the lab. Provide answers to any questions above. Did you have any problems?