OProf

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_ib 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 .