Sequence alignment - Lesson plan

Outcomes

• Understand why alignment is necessary in analyzing biological sequences.
• Understand how alignment is different from exact matching.
• Understand longest common subsequence problem and relationship to sequence alignment.
• Understand relationship between graph traversal and alignment
• Able to modify alignment algorithm for different types of alignments (global/local/etc.)
• Able to implement alignment algorithm with simple scoring scheme
• Understand why backtracking is necessary to find actual alignment
• Understand how scoring functions change alignment algorithm.
• Understand affine gap penalties and alignment strategy

Class Activities

Exercise break 5.14 - team exercise

Discuss greedy change versus bin packing we did on exam.

Go through sequence alignment algorithm on matrix

Discuss linear space alignment

Discuss backtracking

Go through gap scoring strategies

 

Exercises

Rosalind block 5.  5H