CIS-BP PWM Table Format

The CIS-BP PWM Table format is a positional-independence-model format that assumes that each nucleotide position in the binding site contributes independently and additively to the overall binding-free energy of the DNA motif.

This format also assumes that there is only one affinity maxima in the sequence-affinity space of the protein and therefore cannot capture possible different binding modes.

The CIS-BP PWM Table format contains a table of nucleotide probabilities (PWM format) instead of nucleotide relative affinities (PSAM format) or nucleotide counts (TRANSFAC format). This format is similar to the R PSAM format, except that the entries contain probabilities instead of relative affinities. The ADB expects models saved in this format to have a “.cisbp” file extension.

Number of parameters in the model: 3N (where N is the length of the motif)

Here is the complete CIS-BP PWM Table file for a 11 base-pair affinity model:

 

 

Pos     A       C       G       T
1       0.26802966389985        0.024220982446591       0.32950061232821        0.37824874132535
2       0.25428629745544        0.346203565110899       0.368791672336369       0.0307184650972919
3       0.0     0.0     0.0     1.0
4       0.0     0.0     0.922166281126684       0.0778337188733163
5       1.0     0.0     0.0     0.0
6       0.0339501973057558      0.478942713294327       0.381208327663628       0.105898761736289
7       0.0     0.0     0.0     1.0
8       0.0     1.0     0.0     0.0
9       1.0     0.0     0.0     0.0
10      0.00877670431351199     0.19808817526194        0.052320043543339       0.740815076881209
11      0.13627704449585        0.28017417335692        0.26864199210777        0.31490679003946