Finding the Optimal Pairwise Sequence Alignment

Finding the Optimal Pairwise Sequence Alignment

Learning Objective: 

• Given a set of sequences and a scoring framework, students will find the optimal global or local pair-wise alignment.
• After working through the alignment of two DNA sequences using a simple three-part scoring system (in class), students will align a set of amino acids using a more complex scoring system in a follow-up homework assignment.


Students will demonstrate meeting learning objectives through team work assignment and through individual follow up homework.



  1. Introductory PowerPoint slides (based on assigned textbook reading but not assuming much) to describe:
    a)           the reason for aligning sequences and for determining the best possible alignment;
    b)          the magnitude of the problem;
    c)           how to break down the problem to sub-problems, each of which needs to be solved once;
    d)          how to use a matrix to keep track of partial scores.
  1. Break out into existing final project teams of three people each (previously designated by instructor to include individuals from different disciplinary backgrounds); assign one person to be the match calculator, one to be the mismatch calculator, and one to be the gap calculator.
  1. Go to white boards and generate a suitable matrix with initialization scores where the gap penalty = - 1.0.  (Project the sequences to all screens, LCD and projector).
  1. When all teams have produced something useful, project the match and mismatch scoring system to be used in determining the scores in the remainder of the matrix.
  1. Teams will calculate the scores in the matrix by comparing the score for each of the three choices and filling in the highest.
  1. Using the matrix, each team will determine and represent the optimal alignment between the two sequences.