Weight Matrix Definition
- A weight matrix for a pattern of length n is defined as a matrix of numbers Wi,x where i is in {1,2,...,n} and x is in {A,T,G,C} for dna.
- The score of the string x1...xn is given by:
- W1,x1 + W2,x2 + ... + Wn,xn
- For example, the weight matrix for a eukaryotic promotor cap region (Figure 25 of the 1992 edition of the text):
| | -2 | | -1 | | 0 | | 1 | | 2 | | 3 | | 4 | | 5 |
| |
|
| A | | -0.43 | | -5.01 | | 1.34 | | -1.06 | | 0.02 | | -0.12 | | -0.51 | | -0.41 |
| C | | -0.77 | | 1.08 | | -5.33 | | -0.24 | | -0.08 | | 0.13 | | -0.19 | | -0.07 |
| G | | 0.43 | | -4.50 | | -4.50 | | 0.95 | | -4.50 | | 0.02 | | 0.48 | | 0.22 |
| T | | 0.54 | | -5.07 | | -1.67 | | 0.01 | | 0.50 | | -0.10 | | 0.23 | | 0.24 |
| Concensus | | T | | C | | A | | G | | T | | n | | G | | t |
| | G | | | | | | | | | | | | t | | g |
| |
|
| Example | | T | | C | | T | | G | | T | | A | | T | | G |
| Score | | 0.54 | + | 1.08 | + | -1.67 | + | 0.95 | + | 0.50 | + | -0.12 | + | 0.23 | + | 0.22 | = | 1.73 |