
In this directory are input files, parameter files, and output files for 3 example runs of MotEvo
in its TFBS prediction mode.

Input files:
------------
input_ref.fna = 11 proximal promoter regions on chromosome 7 of the human genome.
input.fna = Multiple alignments with other mammals for the same 11 proximal promoter regions.

Weight matrix files:
wms_noweight = file with 3 example mammal weight matrices.
wms_weight = the same 4 WMs but now with different prior weights assigned.

Background model:
bg_order1 = probabilities for a bg-model of order 1 (single neighbor).

Parameter files:
motevoc_params_ref = Parameters for running only on the human sequence, 
using a simple zeroth-order background model, and fixed prior.

motevoc_params = Parameters for the same as previous but now on the
multiple alignment

motevoc_params_prior_bg = In this version MotEvo also estimates the priors and uses a first
order background model read from a file.


Example 1
---------
Here we run only on the human sequence. The priors are the same for all motifs and are fixed. 
A zeroth order background model with equal probabilities for each letter is used. Only sites 
with posterior probability at least 0.2 are printed out.

Command:
../../source/motevo input_ref.fna motevoc_params_ref wms_noweight > report_ref

output files:
report_ref = This contains information on the mode in which MotEvo was run.
sites_ref = Predicted TFBSs.
priors_ref = Predicted priors and densities.

Example 2
---------
Here we run in the exact same way as in example 1, except that we now use multiple alignments
as input. We now use the UFE model, with length 8, and note also that we print out all predicted
UFE sites in the output files.

Command:
../../source/motevo input.fna motevoc_params_ma wms_noweight > report_ma

output files:
report_ma = Information on the mode in which MotEvo was run.
sites_ma = Predicted TFBSs.
priors_ma = Predicted priors and densities.

Example 3
---------
Here we give different priori weights to the input WMs (these are specified by the 'PW' lines in the WM file), 
we use expectation-maximization to fit all the priors, and we use a background model of order 1 that is
read from a file. In addition, we do now omit the UFE sites from the reported sites.

Command:
../../source/motevo input.fna motevoc_params_ma_bg1prior wms_weight > report_ma_priorb1

output files:
report_ma_priorbg1 = Information on the mode in which MotEvo was run.
sites_ma_priorbg1 = Predicted TFBSs.
priors_ma_priorbg1 = Predicted priors and densities.

Note that with prior updating only 1 Snail site remains over the 0.2 posterior cut-off at the end.

