Homework Assignment #1

Due in class 3/11

Part 1: Pairwise Sequence Alignment

Using the BLOSUM 50 substitution matrix, show (a) the alignment matrices, and (b) the returned alignments for the following three cases:
  1. global alignment of the sequence HEART and the sequence HIT with linear gap penalty function where g = -3
  2. global alignment of HEART and HIT with affine gap penalty function where g = -1 and h = -4
  3. local alignment of PARK and SRQ with linear gap penalty function where g = -3
Be sure to illustrate the links followed in the traceback procedure. If there is more than one optimal alignment, return the highroad alignment. For the affine penalty case you should use distinct colors or symbols to indicate into which matrix each link is pointing.

Part 2: Whole Genome Alignment

Consider using MUMmer to align the two toy genomes:
Genome A: atctactt
Genome B: ttatgta
  1. Show the suffix tree for these two genomes.
  2. What are the MUMs for the two genomes?
  3. Show the alignment that would be returned by MUMmer, including the longest subsequence of MUMs, and descriptions of any other key features of the alignment.