Figure 1.

Amino acid PSSM. Amino acid PSSM of length m = 10 of a zinc-finger motif. If the score threshold is th = 400, then only substrings beginning with C or V can match the PSSM, because all other amino acids score below the intermediate threshold th₀ = th - σ₀ = 400 - 398 = 2. That is, lookahead scoring will skip over all substrings which begin with amino acids different from C and V. Here σ_d, d ∈ [0, m - 1] denotes the maximal score that can be achieved in the last m - d - 1 positions of the PSSM as defined in the text.