For the sake of simplicity, we are going to illustrate the mechanisms of RIS 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.
Root insertion sequence elements or RIS elements are short fragments with a function in the first position that transpose to the start position of
genes. The default value for the
RIS transposition rate in GeneXproTools 4.0 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,
you will obtain better results with RIS transposition rates of 1.0.
All RIS elements start with a function, and therefore must be chosen among the sequences of the
heads. For that, a point is randomly chosen in the head and the gene is scanned downstream until a function is found. This function becomes the start position of the RIS element. If no functions are found, the operator does nothing.
The RIS transposition operator randomly chooses the chromosome, the gene to be modified, and the start and termination points of the RIS element.
Consider the following chromosome composed of three genes, each with a head length of 7:
012345678901234012345678901234012345678901234
*a/cadQcabcdaca*aQb/ccccbbaaca/*c-Qd+abccdabb
Suppose that the sequence “-Q” in gene 3 was randomly chosen to become an RIS element. The transposon copies itself and then transposes to the root of the gene, giving:
012345678901234012345678901234012345678901234
*a/cadQcabcdaca*aQb/ccccbbaaca-Q/*c-Qabccdabb
Note that during transposition, the whole head shifts to accommodate the RIS element, losing, at the same time, the last symbols of the head (as many as there
exist in the transposon). In this case, the sequence “d+” was deleted and an extra copy of the transposon was created. As with
IS transposition, the
tail of the gene subjected to RIS transposition and all nearby genes remain unchanged. Note, again, that all the programs newly created by this operator are syntactically correct as it also preserves the
structural organization of the
chromosome.
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