Here is a session using ProfileSearch to search through the entire protein sequence database with a profile generated from a group of aligned 70 kd heat shock and heat shock cognate protein sequences. The profile was generated in the example session from the ProfileMake program. The output file from ProfileSearch is an ordered list of the sequences with the highest alignment scores when compared to the profile. The first section describes the conditions used in running ProfileSearch , the number of sequences examined, and the amount of CPU time used. The second section reports the documentary information from 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.