Scoring Candidate Motifs - Motif Models & Position Weight Matrices Step by Step

A PWM scores a candidate by multiplying its per-column frequencies.

highlighted = computed this step

Score a candidate by multiplying column frequencies

The consensus ACGT scores 1 times 3/4 times 1 times 3/4 equals 9/16.

1\cdot\frac{3}{4}\cdot1\cdot\frac{3}{4}=\frac{9}{16}

The one-mismatch candidate ACGA scores 3/16, while TCGT hits an unobserved first-position T and scores 0.

\text{ACGA}=\frac{3}{16},\quad \text{TCGT}=0

With pseudocount 1, TCGT has nonzero score 5/256. Brute-force search returns ACGT as the best candidate.

\text{score}_{\text{pseudo}}(\text{TCGT})=\frac{5}{256}