Start instructions

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

java -cp .:jstacs-1.3.1.jar:lib/numericalMethods.jar:lib/bytecode.jar:lib/biojava-live.jar projects.dispom.Dispom 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 Dispom 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, OPTIONAL String
position a switch whether to use uniform, skew-normal, or mixture position distribution, range={UNIFORM, SKEW_NORMAL, MIXTURE}, default = MIXTURE String
mean the mean of the a priori TFBS distribution, default = 250.0 Double
sd the sd of the a priori TFBS distribution, valid range = [1.0, Infinity], default = 150.0 Double
motifs the number of motifs to be searched for, valid range = [1, 5], default = 1 Integer
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=', 'best-random-plugin=', 'best-random-motif=', 'enum-all=', 'enum-data=', 'heuristic=', and 'specific=' String=[Integer | String]
adjust a switch whether to adjust the motif length, i.e., either to shrink or expand, default = true Boolean
maxPos a switch whether to use max. pos. in the heuristic or not, default = true Boolean
learning a switch for the learning principle, range={ML, MAP, MCL, MSP}, default = MSP String
threads the number of threads that are use to evaluate the objective function and its gradient, valid range = [1, 128], default = 4 Integer
starts the number of independent starts of Dispom, valid range = [1, 100], default = 1 Integer
xml the file name of the xml file the classifier is written to, default = ./classifier.xml String
p-val a p-value for predicting binding sites, valid range = [0.0, 1.0], OPTIONAL Double

Case studies

In case studies presented in the paper, we started Dispom 50 times. For predicting binding sites, we used 'p-val=1E-4'. For additional information visit the Dispom page at www.jstacs.de