SCANPS has different modes, that implement different types of search. In the current distribution, there are four MODES which have the numbers - 200, 202, 212 and 210. We will concentrate on MODES 200 and 202 which are the most commonly used. MODE 200 searches a protein sequence against a protein sequence database, either with or without iteration and with simple, length-dependent gap-penalties. MODE 202 does the same, but with a more complicated gap-penalty model that has a creation and extension penalty. MODE 200 is the fastest, MODE 202 will typically be more sensitive and give longer alignments.
scanps -mode 200 -s test.fa -probcut 30 -bdb sprot.fas
produced the output in the file: test_200_probcut30.log. The output has a number of sections, the preamble the score list, the pairwise alignments, the multiple alignment and the trailer. The sections are exaplained below: