An evolutionary-based approach for feature generation: Eukaryotic promoter recognition

Prediction of promoter regions continues to be a challenging subproblem in mapping out eukaryotic DNA. While this task is key to understanding the regulation of differential transcription, the gene-specific architecture of promoter sequences does not readily lend itself to general strategies. To date, the best approaches are based on Support Vector Machines (SVMs) that employ standard "spectrum" features and achieve promoter region classification accuracies from a low of 84% to a high of 94% depending on the particular species involved. In this paper, we propose a general and powerful methodology that uses Genetic Programming (GP) techniques to generate more complex and more gene-specific features to be used with a standard SVM for promoter region identification. We evaluate our methodology on three data sets from different species and observe consistent classification accuracies in the 94 95% range. In addition, because the GP-generated features are gene-specific, they can be used by biologists to advance their understanding of the architecture of eukaryotic promoter regions.