Knexus system post-installation instructions
1. You may have to add some items to your Web server to make Knexus work properly.
2. If you have the Microsoft Web server IIS installed and started, the installation program should have updated the server and opening the "Knexus" link on your desktop should take you to the Knexus home page.
3. If you have Apache Web Server installed, you will have to edit the httpd.conf file in order to add the aliased directories necessary to run Knexus.
Add the following lines to httpd.conf and substitute the directory name in which you chose to install Knexus for the word ROOT in the lines below, e.g. "c:\program files\proteometrics": 
    Alias /prowl/ "ROOT/prowl/"
    Alias /PROWL/ "ROOT/prowl/"
    Alias /results/ "ROOT/results/"
    Alias /temp-gif/ "ROOT/temp-gif/"

    <Directory "ROOT/prowl">
        Options Indexes MultiViews
        AllowOverride None
        Order allow,deny
        Allow from all
    </Directory>
    <Directory "ROOT/results">
        Options Indexes MultiViews
        AllowOverride None
        Order allow,deny
        Allow from all
    </Directory>
    <Directory "ROOT/temp-gif">
        Options Indexes MultiViews
        AllowOverride None
        Order allow,deny
        Allow from all
    </Directory>

    ScriptAlias /prowl-cgi/ "ROOT/prowl-cgi/"
    <Directory "ROOT/prowl-cgi">
        AllowOverride None
        Options None
        Order allow,deny
        Allow from all
    </Directory>
After making these changes, save the file and restart the Apache server from the Control Panel, or restart the computer. Double clicking on the "Knexus" shortcut on the Desktop should then take you to the Knexus main page. If this fails, please contact us at 1-204-947-6706 (Canada), 1-212-563-7055 (US) or by email at answers@proteometrics.com
4. As shipped, Knexus is set up to allow dbEST searches, but the dbEST database is not included. You can download dbEST from the source at the National Center for Biological Information at the US NIH using the "NCBI Update" program available on the Start Menu. Run this program and set the Database to "est" in the drop-down menu on top. It will take several hours and require at least 5 Gigabytes of free disk space to download this database.
If you cannot download dbEST for any reason, please contact us and we will send you a recent version on CDs.