There is an essay on profile analysis in the Multiple Sequence Analysis chapter of the Program Manual. TProfileGap works like BestFit but accepts a profile instead of one of the sequences. The symbol comparison values are present in the profile itself and need not be set. The gap and gap length weights specified in TProfileGap are maximum values. The actual position-specific gap penalties at any position are determined by multiplying the gap creation penalty by the percent value in the second to the last column of the profile, and the gap extension penalty by the percent value in the last column of the profile.
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.