Dispom has been implemented within the framework of Jstacs, an open source Java library for statistical analysis and classification of biological sequences. Since Jstacs has been released under GPL 3 (or later), Dispom is distributed under GPL 3 as well. The sources of Dispom can be obtained as part of the Jstacs sources from the Jstacs downloads page. You find the main class of Dispom at projects.dispom.Dispom.java.
Dispom as well as Jstacs are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
java -jar Dispom.jar 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 Dispom with the best from 100 randomly drawn starting values, and search for motif occurrences with a p-value of less than 1E-4
.
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= |
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 |
In addition to the Dispom binary, we also provide a program (DispomPredictor.jar) that can be used to predict binding sites using an already trained classifier. Application of DispomPredictor.jar could be to predict binding sites of a motif found on some set of training data on additional, independent test data, or to test different p-values for predictions without the need to start the training process repeatedly as well.
You can start the Dispom predictor by invoking
java -jar DispomPredictor.jar home=path/to/data/directory/ fg=fgfile.txt bg=bgfile.txt p-val=1E-4 xml=./classifier.xml
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 |
xml | the file name of the xml file the classifier has been written to, default = ./classifier.xml | String |
p-val | a p-value for predicting binding sites, valid range = [0.0, 1.0] | Double |
one-histogram | if no background file is specificed, p-values are computed either using a joint histogram (true), or a sequence-wise histogram (false), default = true, OPTIONAL | boolean |