# DiPoMM - Instructions

Once you have unzipped the archive, you can start DiPoMM e.g. by invoking

`java -cp .:jstacs-1.2.jar:lib/numericalMethods.jar:lib/bytecode.jar:lib/biojava-live.jar projects.DiPoMM home=path/to/data/directory/ fg=fgfile.txt bg=bgfile.txt init=best-random=100 p-val=1E-4`

to search for motifs that are over-represented in `path/to/data/directory/fgfile.txt` but not in `path/to/data/directory/bgfile.txt`, initialize DiPoMM with the best from 100 randomly drawn starting values, and search for motif occurrences with a p-value less than `1E-4`.
Under Windows, you must use ";" instead of ":" in the class path.
The arguments have the following meaning

name | comment | type
home | the path to the data directory, default = ./ | String
ignore | the char that is used to mask comment lines in data files, e.g., '>' in a FASTA-file, default = > | Character
fg | the file name of the foreground data file (the file containing sequences which are expected to contain binding sites of a common motif) | String
bg | the file name of the background data file | String
length | the motif length that is used at the beginning, valid range = [1, 50], default = 15 | Integer
flankOrder | The Markov order of the model for the flanking sequence and the background sequence, valid range = [0, 5], default = 0 | Integer
motifOrder | The Markov order of the motif model, valid range = [0, 3], default = 0 | Integer
bothStrands | a switch whether to use both strands or not, default = true | Boolean
init | the method that is used for initialization, one of 'best-random=', 'enum=', and 'specific=' | String=[Integer | String]
xml | the file name of the xml file the classifier is written to, default = ./classifier.xml | String
adjust | a switch whether to adjust the motif length, i.e., either to shrink or expand, default = true | Boolean
p-val | a p-value for predicting binding sites, valid range = [0.0, 1.0], OPTIONAL | Double

For additional information visit the DiPoMM page at www.jstacs.de