Horizontal sequence :RIVL Vertical sequence:FMK Scoring rules: g/o = -3, g/e = -1, match or mismatch - from PAM250 substitution matrix below. SW algorithm. 1. Complete the scoring matrix. Scoring matrix with PAM250 scores: R I V L F M K 2. Set up, initialize and complete the SW matrix. 3. Retrace, align and score alignment(s). Use the arrows and circles for the matrix and path(s). R I V L F M K Align and score all optimal alignments here. PLZ the arrows and circles for the matrix and path(s) AND SHOW ALL possible Alignment
Horizontal sequence :RIVL
Vertical sequence:FMK
Scoring rules: g/o = -3, g/e = -1, match or mismatch - from PAM250 substitution matrix below.
- SW algorithm.
1. Complete the scoring matrix.
Scoring matrix with PAM250 scores:
| R | I | V | L | |
| F | ||||
| M | ||||
| K |
2. Set up, initialize and complete the SW matrix.
3. Retrace, align and score alignment(s).
Use the arrows and circles for the matrix and path(s).
| R | I | V | L | ||
| F | |||||
| M | |||||
| K |
Align and score all optimal alignments here.
PLZ the arrows and circles for the matrix and path(s) AND SHOW ALL possible Alignment
Here the following points are kept into consideration
1. The opening gap (g/o) is -3 so the first cell is written to be -3.
2. The extending gap (g/e) is -1, so the consecutive cells are increased by -1.
3. The highest from the gaps and the match and mismatch are chosen and then written. It is followed by a arrow from each in order to get the sequencing direction.
4. The scoring value is calculated by using the values from the matrix.
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