In the process of identifying a new GPCR, the sequence analysis will have clearly placed the receptor into one of the three families, and provided strong clues as to further classification. To identify the activating ligand and/or discover the biological function of the receptor, requires in-depth analysis of the sequence at the protein and nucleotide level. The aim of this section is to describe bioinformatic methods, highlight resources, and point to pertinent literature to help determine key features of a receptor sequence. Some protein motifs appear to be specific for small sub-families based on current knowledge, yet, this type of information will increase as the complete set of GPCRs becomes known and, collectively, should become a valuable resource if the data can be captured in searchable form.
The analysis of sequences is broken down into specific sections which, more or less, form a workflow process for an analyst. It is impossible to be exhaustive and cover all methods. Thus, some sections cover the analysis process generally, some are more specific, but where this occurs, it is because in the authors' opinion they represent the future trend for protein family analysis where the emphasis is shifting to specific details crucial to biological understanding and relevance.
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