ProfileSearch compares a profile to a set of sequences and lists the sequences that contain a region similar to the profile. ProfileSegments is used to display an optimized alignment between the best segment of similarity in each sequence in the list and the profile. 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. You can tell ProfileSegments to ignore any of the sequence files in the list by editing this file. If the profile that was used in ProfileSearch cannot be identified and read correctly from the information in the text heading of the input file, ProfileSegments complains and stops.
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.