A set of fixed-length DNA sequences aligned with
respect to a functional site, e.g. a transcription start
site, is scanned in a sliding window in order to determine
the occurrence frequency of a particular sequence motif
(signal) defined by a particular signal. Multiple sets
can be processed at the same time. The output is a graph
showing the occurrence frequency of the signal as a
function of its position relative to the functional sites.

A detailed description of the method can be found

here
**MEME Motif Format**

The motif library provided by **SSA** have been originally downloaded from **The MEME Suite website**. Motifs have then undergone a reformatting process (for more details, please read here).

Matrices from **MEME** are provided in two formats:

- as
**letter-probability** matrices;
- as
**integer log-odds** weight matrices.

The conversion of base counts into weights is given by the formula shown here:

**(1)**
where *f*_{i}_{b} is the relative frequency of base *b* at PWM position *i*, *q*_{b} is the background frequency of base *b*, and *c* is the fraction of pseudo-counts added to the observed base frequencies.

Unless specified otherwise, background letter frequencies are those from a uniform background (A 0.25000 C 0.25000 G 0.25000 T 0.25000).

Weights are rounded to nearest integers to allow for efficient computation of the probability distribution for scores expected from random sequences.

For more details, visit the **MEME website** or our **PWMLib site** .