A profile is a table that contains all of the comparison information of a group of aligned sequences. The profile contains as many rows as there are positions in the aligned sequences. Each row contains a score for the alignment of the corresponding position of the aligned sequences with each possible base or residue. The profile is the input data for ProfileSearch , which can find sequences in the database similar to your group of aligned sequences, and ProfileGap , which can make an optimal alignment between the aligned sequences and another sequence. The aligned sequences may be specified to ProfileMake with an ambiguous file expression or in a list file similar to the input for Pretty or LineUp .
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.