- Strings s1=cctag, s2=catt
| c | c | t | a | g | |||
|---|---|---|---|---|---|---|---|
| 0 | -1 | -2 | -3 | -4 | -5 | ||
| c | -1 | 3 | 2 | 1 | 0 | -1 | |
| a | -2 | 2 | 1 | 0 | 4 | 3 | |
| t | -3 | 1 | 0 | 4 | 3 | 2 | |
| t | -4 | 0 | -1 | 3 | 2 | 1 | |
| s1 | c | - | c | t | - | a | g |
| s2 | c | a | - | t | t | - | - |
| c | c | t | a | g | |||
|---|---|---|---|---|---|---|---|
| 0 | 0 | 0 | 0 | 0 | 0 | ||
| c | 0 | 3 | 3 | 2 | 1 | 0 | |
| a | 0 | 2 | 2 | 1 | 5 | 4 | |
| t | 0 | 1 | 1 | 5 | 4 | 3 | |
| t | 0 | 0 | 0 | 4 | 3 | 2 | |
| s1 | c | t | a | c | a | t | |
| s2 | c | - | a | c | - | t |
Review Vid - 1
MT Content:
- Building matrix alignment
- Global
- Local
- end-gap-free? LCS (longest common subsequence)
- Traceback
Quiz 1 and 2 help for these - Dealing recurrence -> Solve matrix
- Change recurrence based on new requirements
BLAST not on midterm
- Change recurrence based on new requirements
- Lab 1
- Part A, Part D
- FASTQ -> FASTA
- Not so much this one, no quality score
FASTA -> FASTQ
- Part A, Part D
- Simple short answers
- Statistics (E(L) - Longest common subsequence)
Global:
- -for space, -for mismatch, +match
Local: - spaces, mismatch, match
- Forget sections, min=0