Eukaryotic and prokaryotic promoter prediction using hybrid approach

Promoters are modular DNA structures containing complex regulatory elements required for gene transcription initiation. Hence, the identification of promoters using machine learning approach is very important for improving genome annotation and understanding transcriptional regulation. In recent years, many methods have been proposed for the prediction of eukaryotic and prokaryotic promoters. However, the performances of these methods are still far from being satisfactory. In this article, we develop a hybrid approach (called IPMD) that combines position correlation score function and increment of diversity with modified Mahalanobis Discriminant to predict eukaryotic and prokaryotic promoters. By applying the proposed method to Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli, and Bacillus subtilis promoter sequences, we achieve the sensitivities and specificities of 90.6 and 97.4% for D. melanogaster, 88.1 and 94.1% for H. sapiens, 83.3 and 95.2% for C. elegans, 84.9 and 91.4% for E. coli, as well as 80.4 and 91.3% for B. subtilis. The high accuracies indicate that the IPMD is an efficient method for the identification of eukaryotic and prokaryotic promoters. This approach can also be extended to predict other species promoters.