# Related terms

- PWM:
- PSSM:
- odds:
- log-odds:

# Tools and mechanisms

## How to determine the occurrences of motifs in sequences

### \(p\)-value-based

The program computes a log-likelihood ratio score (often referred to incorrectly as a 'log-odds score') for each motif with respect to each sequence position and converts these scores to P-values using dynamic programming (Staden, 1994), assuming a zero-order null model in which sequences are generated at random with user-specified per-letter background frequencies. (default match p-value threshold is 0.0001)

When sequences are longer than 1kb.

### Score-based

Log odds detection threshold, used to determine bound vs. unbound sites (mandatory) example: 8.059752