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When you create a custom design, you can specify your targets of interest in the Define Targets step of the wizard using gene names. The SureDesign gene finder algorithm is responsible for mapping each gene name to a specific region in the target species genome.
If you mark the Allow Synonyms check box when defining your targets, the gene finder first compares the gene name to a table of synonyms. For example, if you type HER2 into the Target input area in the wizard, the gene finder identifies HER2 as a product of the gene ERBB2, and uses ERBB2 to map the genomic location. If you enter multiple gene names that are synonyms for the same gene, SureDesign will merge the targets into a single region prior to probe selection.
After checking for synonyms, the gene finder then locates the genomic location(s) of the gene using the genome annotation databases you selected in the wizard. If a gene has multiple homologs within the target species genome, and the homologs commonly go by the same gene name, gene finder may map the gene to more than one location. In these cases, the target information provided in the Review Targets step of the wizard includes all identified locations (with each location treated as a separate target ID).
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