Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome

Computational methods for automated genome annotation are critical to understanding and interpreting the bewildering mass of genomic sequence data presently being generated and released. A neural network model of the structural and compositional properties of a eukaryotic core promoter region has been developed and its application for analysis of the Drosophila melanogaster genome is presented. The model uses a time-delay architecture, a special case of a feed-forward neural network. The structure of this model allows for variable spacing between functional binding sites, which is known to play a key role in the transcription initiation process. Application of this model to a test set of core promoters not only gave better discrimination of potential promoter sites than previous statistical or neural network models, but also revealed indirectly subtle properties of the transcription initiation signal. When tested in the Adh region of 2.9 Mbases of the Drosophila genome, the neural network for promoter prediction (nnpp) program that incorporates the time-delay neural network model gives a recognition rate of 75% (69/92) with a false positive rate of 1/547 bases. The present work can be regarded as one of the first intensive studies that applies novel gene regulation technologies to the identification of the complex gene regulation sites in the genome of Drosophila melanogaster.