Abstract: The neural network technology has achieved great success in the field of bio-sequence analysis.But a neural network based on MSSE is not the final solution to the problem of predicting DNA binding sites.In this paper, An improved neural network method, ANN-CE, to predict DNA binding sites is presented.It is a three layered back-propagation neural network in which the error function is a cross entropy function.The result shows that the predicted sensitivity and specificity of ANN-CE increased by 11.40% and 11.91% respectively compared with the back-propagation neural network based on MSSE with the same architecture.

Key words: BP neural network, gene regulation, DNA binding site, cross entropy