The scoring matrix values are present in the profile itself and need not be set. The gap creation and gap extension penalties specified in ProfileGap 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. You can create profiles from aligned sequences by means of the ProfileMake program. ProfileGap accepts as its other input one or more sequences of the same type as the sequences used to create 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 one or more sequences 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.