3 Motif search by genetic algorithm
As a motif search method, genetic algorithms (GA) were adopted. GA
realizes probabilistic search by applying genetic operations to a population of
motif candidates represented by binary strings. The genetic operations consist
of crossover, mutation and selection. The MDL principle plays an essential
role in selecting good motif candidates (shorter is better).
4 Parallelism in the motif extraction system
Three kinds of parallelism can be exploited in the motif extraction system;
trial, divide-and-conquer and data parallelism.
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