Installing a Customized Web-Search Using scan_for_matches

Once you have the Custom directory, you need to
  1. Alter the first line of custom.cgi to reference your local Perl.
    Entering which perl from the command line should give you this information.
  2. Make sure that Custom is within the Web space for your local server. You may want to consult with your local support at this stage.
  3. You now need to add the files with the DNA and protein data that you will be searching. Both need to be in fasta format, the protein file names prot.data and the DNA file named dna.data. These files should be copied into the Custom directory.
  4. Make sure that scan_for_matches and show_hits are both in the Custom directory (these are the programs invoked by custom.cgi).
At this point you should be about ready to try referencing custom.cgi from your web browser.

Good luck,
Mark Dsouza and Ross Overbeek