Abstract
A system for utilizing an artificial neural network to predict splice sites in genes has been studied. The neural network uses a sliding window of nucleotides over a gene and predicts possible splice sites. Based on the neural network output, the exact location of the splice site is found using a curve fitting of a parabolic function. The splice site location is predicted without prior knowledge of any sensor signals, like ‘GT’ or ‘GC’ for the donor splice sites, or ‘AG’ for the acceptor splice sites. The neural network has been trained using backpropagation on a set of 16965 genes of the model plant Arabidopsis thaliana. The performance is then measured using a completely distinct gene set of 5000 genes, and verified at a set of 20 genes. The best measured performance on the verification data set of 20 genes, gives a sensitivity of 0.891, a specificity of 0.816 and a correlation coefficient of 0.552.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Baldi, P., Brunak, S.: Bioinformatics, The Machine Learning Approach, 2nd edn. MIT Press, Cambridge (2001)
Burset, M., Guigó, R.: Evaluation of gene structure prediction programs. Genomics 34(3), 353–367 (1996)
Duda, R.O., Hart, P.E., Stork, D.G.: Pattern Classification, 2nd edn. Wiley, New York (2001)
Haykin, S.: Neural Networks, A Comprehensive Foundation, 2nd edn. Prentice-Hall, Englewood Cliffs (1998)
Hebsgaard, S., Korning, P.G., Tolstrup, N., Engelbrecht, J., Rouzé, P., Brunak, S.: Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Research 24(17) (1996)
Kartalopoulos, S.V.: Understanding Neural Networks and Fuzzy Logic. IEEE Press, Los Alamitos (1996)
Snyder, E.E., Stormo, G.D.: Identifying genes in genomic DNA sequences. In: DNA and Protein Sequence Analysis. Oxford University Press, Oxford (1997)
The Arabidopsis Information Resource, http://www.arabidopsis.org
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Johansen, ∅., Ryen, T., Eftes∅l, T., Kjosmoen, T., Ruoff, P. (2009). Splice Site Prediction Using Artificial Neural Networks. In: Masulli, F., Tagliaferri, R., Verkhivker, G.M. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2008. Lecture Notes in Computer Science(), vol 5488. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02504-4_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-02504-4_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02503-7
Online ISBN: 978-3-642-02504-4
eBook Packages: Computer ScienceComputer Science (R0)