Alignments

For orphan receptors (see chapter 10), it is important to know how the sequences align with other members of the GPCR family primarily to provide clues to possible ligands [for a recent example, (Chambers et al. 2000)]. Multiple alignments, however, have many uses, such as the identification of important conserved residues, structure, and function prediction, demonstration of homology and inference of evolutionary relationships. In the case of GPCRs, they have evolved in more than one direction, for example, towards G proteins (as noted in the previous section for muscarinic receptors) and towards ligands, as in the case of histamine receptors (Zhu et al. 2001).

Phylogeny is a specialist subject and accurate analyses are time consuming and best left to specialists. The best alignment will be the one that represents the most likely evolutionary picture but because of the complexity in trying to achieve these, fast approximate methods have been developed (Duret and Abdeddaim 2000). There are many multiple sequence alignment programs and ClustalW (Thompson et al. 1994) is one of the more widely used. It is a progressive global alignment method that is most applicable where the sequences to be aligned are related over their entire length. Alignments can be viewed and annotated using packages such as JalView Clamp (http://ww.ebi.ac.uk/~michele/jalview/), belvu (http://www.sanger.ac.ukPfam/help/belvu_setup.shtml) and Genedoc (Nicholas, http://www.cris.com/~Ketchup/genedoc.shtml). Phylogenetic trees can be generated by a multitude of methods (see http://evolution.genetics.washington.edu/phylip/software.html). The methods PAUP* (http://www.lms.si.edu/PAUP/) (Swofford 1999) and Phylip (http://evolution.genetics.washington.edu/phylip.html) (Felsenstein 2000) are commonly used to calculate consensus trees as can be seen in the examples of the receptor for UDP-glucose (Chambers et al. 2000) and discovery of new receptors from ESTs (Wittenberger etal. 2001). TreeView (Page 1996) is a popular package used to view generated trees on a PC.

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