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Figure 3 | Algorithms for Molecular Biology

Figure 3

From: Evolving DNA motifs to predict GeneChip probe performance

Figure 3

Evolution of breeding population (best 200 of 1000) of regular expressions to find poor GeneChip probes. Each generation the positive training cases are replaced leading to fluctuations in the measured best score (solid line). The error bars show the mean and standard deviation of ten GP runs with identical parameters. Note the chosen run is typical and consistently lies within one standard deviation of the mean (+). Diversity remains high and there are usually few motifs with the same highest score (□). In this run the number of distinct motifs (×) (i.e. egrep search strings) is almost identical to the number of distinct grammars. Size is limited (*), apparently by the tree depth limit [17]. However, even so, the system slows down by (≈ ) as evolution proceeds.

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