file: README.txt
description: getting first started with the jPREdictor

The jPREdictor program is used for defining motifs, searching them on
sequences, weighting motifs using training sets and scoring sequences
using the weighted motifs.

For running the jPREdictor you need a version of Java. Strongly recommended 
is the 1.5 version or newer, because it garantees C++ like performance. The 
jPREdictor can be used in various ways:

- Command line tool: Start it with
    	java -jar jPREdictor.jar -h
    	java -jar jPREdictor.jar -hs
    	java -jar jPREdictor.jar -ho
  to get help on the all parameters available, special tasks or how to
  create an option file, respectively.

- Graphical user interface (GUI): Start the program in the command line with 
    	java -jar jPREdictor.jar
  (no parameters at all) to get the graphical version.

- Applet: either use your browser and open the file 'jPREdictorApplet.html'
  or start the applet viewer:
    	appletviewer jPREdictorApplet.html
  If you trust the applet it looks the same like the GUI, if not, no Browse
  buttons are available and even copy/paste operations are limited.

For further help, please visit the web site
http://bibiserv.techfak.uni-bielefeld.de/jpredictor/
and check the manual section.
