Profile Analysis

Profile analysis uses information from a group of aligned sequences to create a generalized probe, the profile, for sequence or structural motifs. The profile contains information about the location and type of sequence conservation observed in the aligned sequences, the strength of the sequence conservation, and the observed positions of gaps needed to align the sequences, and is most easily understood as a description of the envelope of sequences capable of forming a given motif. When the sequences are aligned based on their three-dimensional structure, the resulting profile describes the sequences capable of folding into such a structure, and is thus a description of the sequence properties of a structural motif. Standard methods of sequence comparison, such as alignment or database searching, can be performed using a profile instead of a single sequence, and can be thought of as the comparison of the consensus of the motif to a sequence or to a database.