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Pseudomonas Genome Database - Gene Numbering Scheme

RNA Gene Numbering Scheme

A new numbering scheme using decimal numbers was proposed to solve the problem of assigning PA numbers to new genes that are inserted between two existing neighbouring genes in the Pseudomonas aeruginosa genome whose PA numbers are in consecutive integers.  This scheme preserves the essential property of the original, solely integer-based system in that the magnitude of the ID reflects the relative position of the gene in the genome.

To insert a new gene, X, first determine the genes that are immediately before and after X, for example, A and B.  Let ID(A) and ID(B) be the PA numbers for genes A and B respectively, and let n be the number of fractional digits of ID(A). The PA number for X, ID(X), can then be determined by the following formula:


This formula essentially says: add 1 to the last digit of ID(A).  If the number obtained equals ID(B), put the 1 to the right of the last digit of ID (A).

Figure 1: Inserting genes between PA1000 and PA1001. First PA1000.1 was inserted between PA1000 and PA1001. Then PA1000.2 was inserted between PA1000.1 and PA1001. Finally PA1000.01 was inserted between PA1000 and PA1000.1.