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An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the FIG ID is used for each gene. Each gene also has a list of aliases. There may be none, or there may be a dozen.

Refseq IDs are included without change, but most of the other aliases use a prefix to identify the type. The prefix ends with either a vertical bar (|) or colon (:). For example, the gene with a FIG ID of fig|100226.1.peg.3361 has the following aliases.

Gene names (e.g. dnaK or grpE) are also considered aliases.