Groups of conserved motifs are excised from alignments and used as fingerprints of family membership. Sequence information is maximised through iterative database scanning, so diagnostic performance increases with each cycle. The advantage of this approach is that residue mismatches are tolerated within motifs, and where a motif is not matched, the framework provided by neighbouring motifs still allows reliable identification. The scanning algorithm interprets the aligned motifs essentially as a series of frequency matrices - i.e., identity searches are made, with no mutation or other similarity data to weight the results. The power of fingerprints is readily appreciated in relation to plots of their profiles against given query sequences.
Sharp peaks appearing in a systematic order, above the level of noise, indicate a positive hit.
This means that the alignments themselves may be analysed further. Searching both databases is thus more comprehensive, and in some cases more effective, since an alternative means of analysis is provided where regular expressions fail. The G-Protein coupled receptor superfamily comprise a large number of membrane bound proteins which have been implicated in many neurotransmitter and hormone related disease states. They are therefore of immense importance to the pharmaceutical industry as therapeutic targets. A brief review of the published approaches to the construction of GPCR models was presented.