
In this directory are input files, a parameter file, and output files for an example
run of MotEvo in its weight matrix refinement mode.

Input files:
input.ctcf.aln = alignments of 450 regions in the human genome that were found (by ChIP-seq)
to be bound by the transcription factor CTCF. Aligned with orthologous regions from 6 other
mammals.

wm_ctcf.org = Original WM for CTCF as obtained in Drosophila.


Command:
../../source/motevo input.ctcf.aln motevoc_params wm_ctcf.org > report

Note: We run with only 1 input WM (CTCF) and the UFE model. The UFE model gets an a prior weight 200 times higher
than the CTCF WM, and the bg prior is 0.99. In the WM iteration only sites with posterior at least 0.5 are used.
By default we typically choose the length of the UFE the same as the WM we are refining. 

output files:
report = Report provided by MotEvo of the parameters it read in, its running mode, etc.
sites = Final predicted sites using the updated WM.
priors = Final predicted number of sites and site densities.
wms.updated = The refined CTCF weight matrix.

Note, for the users information we also include PNG image files of the sequence logos of
the original and refined WMs:
ctcf.org.png
ctcf.refined.png

