For the sake of simplicity, we are going to illustrate the mechanisms of IS transposition
using the compact, linear representation of chromosomes used to describe the
structural organization of
chromosomes in the previous chapter. In this representation, each element (function or terminal) is represented by a single character so that each element can be easily identified by its position in the chromosome.
Insertion sequence elements or IS elements are short fragments of the genome with a function or terminal in the first position that transpose to the
head of genes except the root. The default value for the
IS transposition rate in APS 3.0 is 0.1, as this operator is usually used together with other, more powerful operators such as
mutation. But if you want to introduce genetic modification by using this operator alone, the better results are obtained with IS transposition rates of 1.0.
Any sequence in the genome might become an IS element and, therefore, these elements are randomly selected throughout the chromosome. A copy of the IS element
is made and inserted at any position in the head of a
gene, except the first position.
The IS transposition operator randomly chooses the chromosome, the start and termination points of the IS element, and the target site.
Consider the following chromosome composed of three genes, each with a head length of 7:
012345678901234012345678901234012345678901234
/cQQ*b+bccabdaaQb/Qdd-dcbdbadd-*dQc+bccaabaad
Suppose that the sequence “Qc+” in gene 3 (positions 3-5) was picked up as an IS element to be then inserted between positions 1-2 in gene 2, obtaining:
012345678901234012345678901234012345678901234
/cQQ*b+bccabdaaQbQc+/Qdcbdbadd-*dQc+bccaabaad
Note that, in this case, a perfect copy of the transposon appears at the site of insertion. Note also that a sequence with as many symbols as the IS element is deleted at the end of the head of gene 2 (in this case, the sequence
“dd-” was deleted). Thus, despite this insertion, the structural organization of chromosomes is maintained and, therefore, all the new individuals created by IS transposition are syntactically correct programs.
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