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
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.| 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= |
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 |