>>java -classpath . -jar MotifSearch.jar "-cp ." only works with unzipped jar files. In your case, I would use:
java -cp xerces.jar:biojava.jar:<otherjarshere> -jar MotifSearch.jar Hope that helps, Rahul _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
