The interface to SCANPS follows a fairly standard Unix command style. If you are used to using Unix, then this should be easy. By default, output goes to stdout and so can be piped to other programs for processing. If you are not happy with the Unix command line, then it should be easy for someone to hide this interface behind a WWW form, or other windowing interface. This has been done at the European Bioinformatics Institute (http://www.ebi.ac.uk). We also run a server at Dundee (http://www.compbio.dundee.ac.uk).
SCANPS is controlled by a set of keyword, value commands. The commands may either be specified in a defaults file (scanps_defaults.dat), or on the command line. Values specified on the command line override the defaults set in the scanps_defaults.dat file. The scanps_defaults.dat, scanps_alias.dat and scanps_gapdefs.dat files must all reside in the directory pointed to by the environment variable SCANPSDIR. If SCANPSDIR is not defined, then the program assumes that these files are in the user's current directory. Thus, an installation can have a central set of defaults which may be overridden by individual users who may copy and modify their own copies of the scanps_defaults.dat, scanps_alias.dat and scanps_gapdefs.dat files.