Exercises For Week Two

What I want you to do for this week is really an extension of what we did in lab— a chance to practice, and to use some of these tools in an exploratory way.

1) Find 6 homologous sequences (you can choose a protein of interest, or you can use the histones we used last time), and download them both as nucleotide sequences and as amino acid sequences.

2)Using clustal W, align the amino-acid sequences. Think a bit about what the parameters that you can control might mean, and try the alignment using at least two different parameter sets. Evaluate the resulting alignments, and discuss briefly why your parameter setting did/did not make a difference to the resulting alignment.

3)Take the 2 most closely related sequences (most similar), and do a pairwise alignment using ALIGN of those two sequences (amino-acid sequences). Does the pairwise alignment match the alignment of the two sequences you got using CLUSTAL? Why, or why not?

4) Now take the DNA sequence data for the two most closely related sequences, and align them using ALIGN. Does the resulting alignment appear to match the one you obtain when you align using amino acid sequences? Under what circumstances might those two alignments differ?

5) Finally, run a pairwise alignment of the two most similar sequences using LALIGN. Does the output match the results you obtained in (3)? Under what circumstances would you expect these alignments to differ dramatically.

TODAY'S HINT: The READSEQ tool is your friend. Oftentimes, you cannot tell what is wrong with the format of your input — only that the computer is getting all choked up. Use READSEQ as a way to scrub and polish your sequences. Get to know the parameters you can set.