Genetic algorithms for DNA sequence assembly.
This paper describes a genetic algorithm application to the DNA sequence assembly problem. The genetic algorithm uses a sorted order representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, are tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.
Parsons
R
R
Los Alamos National Laboratory, Computer Research Applications Group, NM 87545, USA.
Forrest
S
S
Burks
C
C
D000465:Algorithms; D003198:Computer Simulation; D008433:Mathematics; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software