I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability
If I have a sequence say "AAPGTGASMHSGLLW" how would I score it against the matrix? I tried taking the product of probabilities corresponding to the matrix, but I end up with a really small number
Any ideas?
Edit:
Consider the simple matrix:
1 2 3 4
A 0.3 0.90 0.5 0.0001
B 0.2 0.05 0.4 0.2
C 0.5 0.05 0.1 0.8
The best match is, with a score of:
CAAC = 0.5 * 0.9 * 0.5 * 0.8 = 0.18
If you change the first letter to an B instead of C
you get a match, with a score of:
BAAC = 0.2 * 0.9 * 0.5 * 0.8 = 0.072
Which is a huge difference for such a small change... This is even worse with my larger matrix since the score is easily affected by small probabilities