BC - Sequence alignment

Sequence alignment can be used to:

• Sequence genomes cheaper and faster

• Find the most recent common ancestor for 2 different species

• Fill in mising gaps present in the fossil record

• Knock-out genes to see what effect they have

Needleman–Wunsch algorithm...

• aligns sequences end to end

• finds the best local alignment

• requires a linear gap penalty

• time complexity is linear in the size of the input sequences

If using Needleman–Wunsch algorithm, the missing score is:

• 0

• 1

• 2

• 3

How many optimal global alignments will results from this matrix?

• 1

• 3

• 4

• 5

Smith-Waterman algorithm...

• aligns sequences end to end

• finds the best local alignment

• finds exactly one alignment

• traces back for the lower right of the dynamic programming matrix

If using Smith-Waterman algorithm, the missing score is:

• 0

• 1

• 2

• 3

Dynamic Programming makes me feel...

• Happy

• Sad

• Anxious

• Smarter