Paralogs refer to genes that appear in more than one copy in the genome of a given organism (1). Paralogs arise from gene duplication events. If it is advantageous, duplicated genes evolve independently to produce distinct but related proteins. This process often involves specialization of paralogous genes into specific functions (1). The evolution of paralogous genes can generate developmental and physiological novelties by changing the patterns of regulation of these genes, by changing the functions of the proteins they encode, or by both (1).

From the complete genomic sequence of a given species, it is possible to identify the paralogous genes in that species. This chapter describes an example of how to map and obtain a graphical representation of paralogous genes in a genomic DNA. The example uses the genome browser at the University of California

From: Methods in Molecular Biology, vol. 338: Gene Mapping, Discovery, and Expression: Methods and Protocols Edited by: M. Bina © Humana Press Inc., Totowa, NJ

at Santa Cruz (UCSC) (2,3). In the analysis paralogy is defined on the basis of significant scores obtained for global alignments of amino acid sequences. This can be contrasted with local alignments, which are often utilized for the discovery of conserved motifs in the amino acid sequences of proteins (see, for example, ref. 4). The example given provides a relatively simple case, a good starting point for a beginner in the field. More complex cases would require additional tool sets. As an example, see the publication that describes how to explore relationships and mine data with the browser at UCSC (5).

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