Flanking Gene Method
The flanking gene method is a procedure in which possible transposed genes are identified by comparing two neighboring syntenic gene pairs. An example visualization of this method is shown to the right. In this visualization, a pair of genes (numbered 1 and 2) in Species A is being compared to an orthologous pair of genes (similarly numbered 1 and 2) in Species B.
In the procedure, sequential, adjoining genes (genes 1 and 2) are compared between two species (A and B). If said genes are from orthologous regions, one would assume the genes remain sequential. However, in a transposition event another gene (eg, gene X in red) inserts itself between two otherwise sequential genes. In this case, gene X is a possible transposed gene, identified by its presence in Species B between genes 1 and 2 which would be otherwise adjoining each other. This method of identification is previously described in Freeling et al 2008.