crossover operator for evolutionary algorithm

Question

[Moses]

Hi everyone,

I'm trying to implement a heuristic approach to improve pairwise sequence alignment. I'm thinking of a crossover operator, to crossover between two sequences. each solution in the population is a pairwise alignment. the length of the alignment is fixed. I have the same number of gaps in all the different solutions. the solutions differ in the number positions of gaps.

How can I crossover between two solutions? any suggestions?

Answer 1

[Jean-Karim Heriche]

In evolutionary algorithms, solutions are typically represented by chromosomes. Trying to formulate the problem in terms of chromosomes would make things easier. If a chromosome is an entire alignment then a simple crossover would be some sort of combination of two parent alignments. By the way, alignment by a genetic algorithm has been tried before e.g. SAGA. You could have a look at how they do it there.