INCLUSive Motif Model

Description

The following description of the INCLUSive_Motif_Model format is taken directly from the MotifSuite web site.

The file must start with a comment line which identifies the format (#INCLUSive Motif Model v1.0).
Next follows the PWM description of a first motif, starting with some comment lines. The first comment line describes a unique motif identifier (#ID). The second comment line shows a motif score (#Score) which can be a score that is computed from the PWM or any other score that reflects the importance of the motif being described. The following two lines give the PWM length (#W) and a consensus description (#Consensus) of the motif. A consensus description is derived from the information available in the PWM; it is a string-based sequence representation of the motif in IUPAC code symbols (A,C,G,T,n,s,w) that describes the most likely nucleotide(s) on each position in the motif (n = any of A,C,G,T, s = C or G, w = A or T. Note that MotifLab can use additional IUPAC codes as well).

The comment lines are immediately followed by the values that make up the PWM (matrix) : each line describes the tab-separated probabilities (Pr) for nucleotide A, C, G and T on a given position in the motif. The number of lines must equal the length of the motif (#W). The probabilities described in a PWM can be frequencies (normalized values between 0 and 1 and the sum of a row equals 1), or they can be represented as counts (values can be higher than 1 and zeros are also common).
MARK : decimal numbers in a PWM must be described using a DOT (not a comma) e.g. 0.54 (not 0,54).


The motif description ends with a blank line return. The second and following motifs are described in exactly the same way, each time separated from each other by a blank line. The end of the file is recognized by the last blank line return. Note that there is no explicit numbering of the motifs in the file.

Example: