Jaspar PWM Formats

The Jaspar PWM formats are positional-independence-model formats that assume that each nucleotide position in the binding site contributes independently and additively to the overall binding-free energy of the DNA motif.

These formats also assume that there is only one affinity maxima in the sequence-affinity space of the protein, and therefore cannot capture possible different binding modes.

The Jaspar PWM formats contain a table of nucleotide counts (TRANSFAC format), instead of nucleotide relative affinities (PSAM format) or nucleotide probabilities (PWM format). The ADB expects models saved in this format to have a “.jaspar” file extension.

Number of parameters in the model: 4N (where N is the length of the motif)

Here are the two versions of the complete Jaspar PWM files for the same affinity model:

 

“Raw” Format

>MA0048

13 13 3 1 54 1 1 1  0 3 2 5 
13 39 5 53 0  1 50 1 0 37 0 17 
17 2 37 0 0 52 3 0 53 8 37 12 
11 0 9 0 0 0 0  52 1 6 15 20

 

“JASPAR” Format

>MA0048

A [13 13 3 1 54 1 1 1  0 3 2 5 ] 
C [13 39 5 53  0 1 50 1 0 37 0 17 ] 
G [17 2 37 0 0 52 3 0 53 8 37 12 ] 
T [11 0 9 0 0 0 0  52 1 6 15 20 ]