Setting Up Your Own Service

You can easily set up your own web site, allowing access to your data using the scan_for_matches software, which is the pattern matching component of PatScan.

Please note: This version is primarily intended to be used by you to search your own files using your internet browser. While it can be used to make your files open to pattern searches by public access it is not designed for this. You should consult you local computer support to check about security issues.

You need to ftp the scan_for_matches library and ftp the skeletal CGI/HTML forms.

Using anonymous ftp this would go as:

```
ftp info.mcs.anl.gov
```
enter
```
anonymous
```
at the "Name" prompt
enter your e-mail address as your password
enter
```
cd /pub/overbeek/PatScan
```
enter
```
get scan_for_matches.tar.Z
```
enter
```
get custom.tar.Z
```
enter
```
bye
```
to exit.

Now, you need to extract the files:

Use the uncompress utility
```
    uncompress custom.tar.Z
    uncompress scan_for_matches.tar.Z
```
to get the files custom.tar and scan_for_matches.tar

Use the tar utility

    tar -xvf scan_for_matches.tar
    tar -xvf custom.tar

to expand the tar files. This creates the directories ScanForMatches and Custom The directory ScanForMatches should contain the following files:

    README              -   how to run the program

    scan_for_matches.c  -   one of two source files
    ggpunit.c           -   the second source file

    run_tests           -   a perl script used to test the downloaded program
    testit              -   a perl script used for testing
    test_prot_patterns  -   test patterns for proteins	
    test_prot_input     -   test protein sequences
    test_output         -   desired output from the test
    test_dna_input      -   test sequences for DNA
    show_hits           -   a perl script used to reformat output

You will need to compile the scan_for_matches software. Follow the instructions in the README file until you have an executable scan_for_matches file, and test it using run_tests.

The directory Custom should contain the following files:

    README
    cgilib.pm
    custom.cgi
    getting_scan_for_matches.html
    interpreting_output.html
    matching_nucleotides.html
    matching_proteins.html
    rules_for_patterns.html

Follow instructions in the README file.

Your data should be in fasta format in the Custom directory, in files called

prot.data -- for proteins
dna.data -- for dna

though you may choose to change this (in the file custom.cgi).

It really is not much effort to set up the web application, and you are welcome to use it for whatever purposes you like.