ProfileScan uses the method of Gribskov et al. 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. For further information about this motif, consult the . . . If ProfileScan rejects your protein sequence, see Appendix VI for information on how to change or set the type of a sequence.
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.