## 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.

• 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.

## Assessment:

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

## Logistics:

- 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.

- 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.

- 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).

- 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.

- Teams will calculate the scores in the matrix by comparing the score for each of the three choices and filling in the highest.

- Using the matrix, each team will determine and represent the optimal alignment between the two sequences.