PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true functional sites. Positional priors tracks can be constructed by manipulating, comparing and combining information about various features, including for instance phylogenetic conservation, DNase hypersensitive sites, repeat regions, nucleosome positions and other epigenetic data, physical properties of the DNA helix, distance from transcription start site or proximity to other known binding sites and many more. Data can be downloaded from the UCSC Genome Browser (or imported from file) and visualized with the graphical user interface. It is also possible to perform de novo motif discovery or motif scanning with known motif models by interfacing with locally installed programs. The results can then be visualized, analyzed and post-processed within PriorsEditor.

PriorsEditor can also be run from the command line without starting up the GUI.
The command to run PriorsEditor in this way is:
java -Xms256M -Xmx256M -classpath PriorsEditor.jar priorseditor.engine.PriorsEditor

In addition you need to provide a protocol script (option -p) and a file describing which sequences to analyze (option -s) You can also specify a log-file with the "-l <filename>" option. All messages will then be written to this file instead of STDERR.

To obtain output from PriorsEditor when run from the command line, the protocol script has to contain "output" commands for all the data you want to keep. For instance, if the protocol script contains a line: "results = output BindingSites in GFF format",
the data from the BindingSites track will be saved to the file "results.gff" (the filename is the same as the name of the output data object and the file-suffix is set depending on the data format used)

Requirements:
* Java

The license of this software is Freeware, you can free download and free use this calculator software.