The GPCRs in the GPCRDB are found and classified by using a profile-based blast method, which is similar to the RPS-BLAST program. Using this profile blast method, all sequences in the UniprotKB database (longer than 300aa) are scored against each profile and depending on the score are either discarded or classified and incorporated. Fragments are discarded, so only proteins which have the complete transmembrane domain present are incorporated.
The alignments in the GPCRDB are made by WHAT IF. This program uses an iterative profile alignment method as described in:
The profiles used to search for GPCRs are the same profiles used for creating the multiple sequence alignments.