MatrixREDUCE 2.0 PSAM XML Format

The MatrixREDUCE 2.0 PSAM 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 MatrixREDUCE 2.0 PSAM format contains a table of nucleotide relative affinities (PSAM format), instead of nucleotide probabilities (PWM format) or nucleotide counts (TRANSFAC format). The ADB expects models saved in this format to have a “.mxr” file extension

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

Here is the complete MatrixREDUCE PSAM file for a 20 base-pair affinity model:

<?xml version="1.0" encoding="ISO-8859-1"?>
<matrix_reduce>
<meta>
<source>MatrixREDUCE v2.0</source>
<comment>xl2134@columbia.edu</comment>
<date>Sat Sep  5 13:30:47 2009</date>
<topology>XXXXXX</topology>
<seed_motif>ACGCGT</seed_motif>
<measurement_file>Spellman1998AlphaTimeCourse.tsv</measurement_file>
<experiment_name>alpha_factor_release_sample016</experiment_name>
<experiment_column>4</experiment_column>
<bonferroni>1562620</bonferroni>
<p_value>0.001</p_value>
</meta>

<directionality>forward</directionality>
<psam_length>20</psam_length>
<optimal_sequence>ACGCGT</optimal_sequence>

<psam>
   # A            C            G            T             # no. opt 
   # +============+============+============+============ # ==+===+==
   1	0.85969796884753	0.875522530539211	0.966215658945203
   1	0.83215662669888	0.870164797284493	0.935033816981325
   1	0.834202316659436	0.8935170481659	0.912719282284239
   1	0.743765763057248	0.810235919424424	0.863430249706623
   0.895227227465743	0.811918862932376	0.911859328855217	1
   0.639343787464176	0.864271645947162	1	0.842416734897722
   0.725596884123757	0.621664281140539	0.826216068102234	1
   1	0.308164140388727	0.461568910245156	0.64081473137858
   0.175147442679764	1	0.313637539653356	0.636890283448217
   0.60139924792208	0.398722213612229	0.306737220226293	1
   0.513679480943895	0.519472777042505	0.568685674850866	1
   1	0.656676034905548	0.700717550011752	0.217280245643776
   1	0.889502833983057	0.444559691503084	0.887768380887137
   1	0.630847204366456	0.684276192196461	0.73443073091296
   1	0.541001312591024	0.739634193559772	0.742945259344238
   1	0.615846375588182	0.693966449775326	0.69130346936043
   1	0.655576270243664	0.691496389212478	0.891572631582694
   1	0.751628504406949	0.739321885823261	0.910096369554558
   1	0.773624494104278	0.742452141493945	0.94601064150157
   1	0.731726438004119	0.745456120745361	0.887664968615272
   </psam>
</matrix_reduce>