Profiles

A very powerful technique for characterizing the putative structure and function of a sequence is the Profile Analysis ( [2]). Profile analysis is a sequence comparison method for finding and aligning distantly related sequences. The comparison allows a new sequence to be aligned optimally to a family of similar sequences. The comparison uses a scoring matrix and an existing optimal alignment of two or more similar protein sequences. The group or ``family'' of similar sequences are first aligned together to create a multiple sequence alignment. The information in the multiple sequence alignment is then represented as a table of position-specific symbol comparison values and gap penalties. This table is called a profile. The similarity of new sequences to an existing profile can be tested by comparing each new sequence to the profile using a modification of the Smith/Waterman algorithm.