Setting Up Your Own Scanning Environment

You may wish to scan your own collections of data for a specialized set of patterns, in which case you might do well to just take our pattern matching program and use it on your machines. The pattern matcher used by PatScan is a fairly small C program called scan_for_matches.

On my Sun, the procedure is fairly simple:

FTP the library to your site. It is contained in the one file scan_for_matches.tar.Z
You could also do this using anonymous ftp:
1. ```
ftp info.mcs.anl.gov
```
2. enter
```
anonymous
```
  at the "Name" prompt
3. enter your e-mail address as your password
4. enter
```
cd /pub/overbeek/PatScan
```
5. enter
```
get scan_for_matches.tar.Z
```
6. enter
```
bye
```
  to exit.
Use the uncompress utility
```
    uncompress scan_for_matches.tar.Z
```
to get the file scan_for_matches.tar

Use the tar utility

    tar -xvf scan_for_matches.tar

to expand the tar file. This creates a directory ScanForMatches which contains 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

Follow instructions in the README file. It really is not much effort to set up, and you are welcome to use it for whatever purposes you like.