Nucleic Acids Research, 1995, Vol. 23, No. 9 1632-1639
© 1995
COMPUTATIONAL BIOLOGY |
Identification of ribosome binding sites in Escherichia coli using neural network models
Neuroscience Program (151 B), Stanford University Stanford, CA 94305, USA 1National Cancer Institute, FCRF Building 469, Room 151, PO Box B, Frederick, MD 21701, USA
* To whom correspondence should be addressed
Received August 26, 1994. Revised February 8, 1995. Accepted February 8, 1995.
This study investigated the use of neural networks in the identification of Escherichia coll ribosome binding sites. The recognition of these sites based on primary sequence data is difficult due to the multiple determinants that define them. Additionally, secondary structure plays a significant role In the determination of the site and this information is difficult to include in the models. Efforts to solve this problem have so far yielded poor results. A new compilation of E.coll ribosome binding sites was generated for this study. Feedforward backpropagatlon networks were applied to their identification. Perceptions were also applied, since they have been the previous best method since 1982. Evaluation of performance for all the neural networks and perceptrons was determined by ROC analysis. The neural network provided significant improvement In the recognition of these sites when compared with the previous best method, finding less than half the number of false positives when both models were adjusted to find an equal number of actual sites. The best neural network used an input window of 101 nucleotides and a single hidden layer of 9 units. Both the neural network and the perceptron trained on the new compilation performed better than the original perceptron published by Stormo et al. in 1982.