There is an essay on profile analysis in the Multiple Sequence Analysis section of the Program Manual. These motifs are represented as profiles in a library. ProfileScan aligns each profile motif to the sequence, and displays all alignments between the profile and sequence that have a normalized score above a set threshold. Aligning to zinci.prf . The .sum file simply lists the number of occurrences of each motif in the sequence of interest.
LineUp is a multiple sequence editor used to create multiple sequence alignments.
Pretty displays multiple sequence alignments. ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for new sequences with similarity to the group of aligned sequences. ProfileGap makes optimal alignments between a sequence and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.