FindM

A set of fixed-length sequences located at the same relative position with respect to a functional site (eg. a transcription start site) is scanned for occurrences of a given motif. The motif may be defined by a consensus sequence or a weight matrix. The search may be confined to a sub-region within the sequences supplied. The program returns either the sequences containing the motif, the sequences not containing the motif, or the sequence regions around the motif.
See the here for further detail.

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 .