Question 11
Consider dynamic programming to do a manual alignment of the following sequences: AGTGT and TATGT. Fill up the score matrix (or grid) below, and calculate the number of entries in the matrix/grid with the value 2. The entry in the grid corresponds to the score of the best-scoring alignment between the -length prefix of first string and -length prefix of second string. Scoring is done as follows:
- For each match between two symbols: point
- For each mismatch between two symbols: point
- For each removal of symbol from any one sequence: point
| T 1 | A 2 | T 3 | G 4 | T 5 | |
|---|---|---|---|---|---|
| A 1 | |||||
| G 2 | |||||
| T 3 | |||||
| G 4 | |||||
| T 5 |