README

(this example covers only use on unix/linux platforms with

the java virtual machine installed.)

1. Copy Program.zip to a directory on your computer.
2. Go to the directory where you saved the file.
3. Unzip the files
4. There are four .jar files among the unzipped files, these must be included in your classpath, this

might be done with these four command lines:

setenv CLASSPATH $CLASSPATH:$HOME/path to your directory/biojava.jar

setenv CLASSPATH $CLASSPATH:$HOME/path to your directory/bytecode.jar

setenv CLASSPATH $CLASSPATH:$HOME/path to your directory/jakarta-regexp.jar

setenv CLASSPATH $CLASSPATH:$HOME/path to your directory/xerces.jar
(where “path to your directory” is the path to the directory where the .jar files are, if you do it this

way it must be done every time you restart your computer, you might add them once for all in

your .envir file)

5. In the same directory as you saved the program type “java Invoke” and press ENTER
6. When you specify the filename you wish to search, you have to give the entire path,

unless the file is in the directory where you run the program from.

The “tilde” character does not work when specifying the path.

(Easiest is to download the file of the 490 intergenic regions of E.coli found on this website

and save it in the same directory as where the program is, then you can call it by its name,

without having to include the path

7. The program will crash if you do not select one or more consensus sequence to search for.