To do this, type:
scanps -ssh2.seq > sh2.scan
The -s tells the program to read the query sequence from the file sh2.seq. The results of the scan will be saved in the file sh2.scan. On a Silicon Graphics R4000 ``Indy SC'' using the PIR38 database which contains 61,248 sequences this scan takes about 580 seconds. On a Sun SPARCstation 2 the scan takes about 3-4 times longer.