The advent of large-scale cDNA and genome sequencing efforts has revolutionized how we identify new genes and has also helped established the discipline of bioinformatics as a major component of both academic and industrial research programs. The mining for novel GPCRs is a good case in point with both industrial and academic researchers utilizing expressed sequence tag (EST) and genomic sequence data (see later) as their starting point to hunt for new receptors. In recent years bioinformatic search strategies have yielded the second GABAb receptor subunit (Jones etal. 1998; Kaupmann etal. 1998; see chapter 28), the human orexin receptors (Sakurai et al. 1998) and the third and fourth histamine receptors [reviewed by (Hough 2001); see chapter 17] to name just a few examples.
In the following chapter we intend to describe how bioinformatics tools can be applied to the identification, characterization, and disease association of GPCRs. The chapter is intended to provide an overview of the applications, tools, and methodologies required to identify and characterize GPCR sequences at both the DNA and protein level. Although focused on GPCRs the techniques are also applicable to other gene families.
Many of the tools described are available for free public use on the internet. However, access to a UNIX based computer system greatly enhances the depth of bioinformatic analysis that can be achieved as many of the tools have been developed for implementation on this system. A good starting guide both to bioinformatic tools and setting up a bioinformatic UNIX work station can be found in 'Developing Bioinformatics Computer Skills' (Gibas and Jambeck 2001).
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