Multiniche Crowding in Genetic Algorithms and Its Application to the Assembly of DNA Restriction-Fragments

Abstract

The determination of the sequence of all nucleotide base-pairs in a DNA molecule, from restriction-fragment data, is a complex task and can be posed as the problem of finding the optima of a multimodal function. A genetic algorithm that uses multiniche crowding permits us to do this. Performance of this algorithm is first tested using a standard suite of test functions. The algorithm is next tested using two data sets obtained from the Human Genome Project at the Lawrence Livermore National Laboratory. The new method holds promise in automating the sequencing computations.