All ProteinProspector programs are implemented according to the Common Gateway Interface (CGI) standard. Hence the HTML form interface can be bypassed in automated settings as long as the programs receive their input in a manner which mimics the CGI format.

To facilitate such efforts this document provides a list of all the name-value pairs associated with the input variables for each program. Future development efforts will refrain from changing these parameters unless absolutely necessary.

An alternative to using the CGI method is to run the programs from the command line. To do this each name value pair needs to be a separate argument. For example to run FA-Index from the command line on a Windows system you can use something like this:

faindex.cgi - create_database_indicies=1 database=SwissProt.11.02

On a UNIX system you should use a command of the following form (run from the directory):

./faindex.cgi - create_database_indicies=1 database=SwissProt.11.02

Note that the first argument has to be a dash character.

When doing this you need to be careful that any characters in the command line are not interpreted by the command line interpreter. For example if a value contains a space the interpreter needs some way of knowing that this isn't the next argument. To get round this any "special characters" have to be encoded. One way of doing this is to use the same encoding as that used in the CGI method.

A useful book explaining CGI programming is:

CGI Programming on the World Wide Web, Shishir Gundavaram, O'Reilly, 1996