Profile Alignment
Profile-profile scoring and alignment is analogous to pairwise sequence comparison, except that the objects being compared are profiles: matrices of real values, representing the probability of amino acids at each position in a corresponding multiple sequence alignment. Our experiments show that profile-profile methods can provide greater sensitivity in homolog recognition and also more accurate alignments of pairs of protein sequences, and also (modest) improvements over alignments of individual sequences to profiles.
Papers from our lab on this topic
Edgar, R., and Sjölander, K., "COACH: profile-profile alignment of protein families using hidden Markov models," to appear in Bioinformatics.
Edgar, R. and Sjölander, K., "A comparison of scoring functions for protein sequence profile alignment," to appear in Bioinformatics.
Supplemental material for Edgar and Sjölander, A comparison of scoring functions for protein sequence profile alignment