Gene family databases

Use functional annotation databases to provide insights into the putative functions of the selected genes and gene families and analyze the target structures for possible binding sites, active sites, and other functionally important domains. 

An increasing emphasis on comparative genomics can be seen in the development of databases covering a broad spectrum of gene families, as well as specialist databases devoted to individual gene families (for example, the MEROPS protease database). 

This approach is illustrated in the phosphodiesterase gene family tree presented in Fig. 8.4. The set of relationships has been determined by comparing not just two sequences with each other, or a database of sequences to one sequence (as in a sequence database search), but by comparing a set of phosphodiesterase sequences to each other in the form of... 

There are other approaches to family databases that rely more extensively on sequence similarity to define classes of genes or proteins. For example, PROSITE (49) is a resource that uses regular expressions to define patterns of residues that represent biologically significant sequence motifs. Recent versions have incorporated profiles, weight matrices that express the characteristics of a gene... 

Table 6.1 PDB representation of selected human gene families of different sizes. Human gene information is from Ensembl Genome Database (NCBI36)...

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