There is an essay on profile analysis in the Multiple Sequence Analysis chapter of the Program Manual. ProfileSearch compares a profile to a set of sequences and lists the sequences with similarity to the profile. ProfileSegments then makes an optimal alignment to display the best segment of similarity in each sequence in the list. The scoring matrix values, gap creation penalties, and gap extension penalties used to find the best region of similarity between the profile and the sequence are all present in the input file itself and need not be set.
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 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.