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Bioinformatics Vol. 18 no. 90002 2002
Pages S75-S83
© 2002 Oxford University Press

Feature subset selection for splice site prediction

Sven Degroeve 1, Bernard De Baets 2, Yves Van de Peer 1 and Pierre Rouzé 3

1 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), K.L. Ledeganckstraat 35, Gent 9000, Belgium
2 Department of Applied Mathematics, Biometrics and Process Control, Universiteit Gent, Coupure links 653, Gent 9000, Belgium
3 Laboratoire associé de l'INRA (France), K.L. Ledeganckstraat 35, Gent 9000, Belgium

Received on April 18, 2002 ; accepted on June 15, 2002

Motivation: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a review and references). These algorithms need information sources or features from which the models can be computed. For splice site prediction, the features we consider in this study are the presence or absence of certain nucleotides in close proximity to the splice site. Since it is not known how many and which nucleotides are relevant for splice site prediction, the set of features is chosen large enough such that the probability that all relevant information sources are in the set is very high. Using only those features that are relevant for constructing a splice site prediction system might improve the system and might also provide us with useful biological knowledge. Using fewer features will of course also improve the prediction speed of the system.

Results: A wrapper-based feature subset selection algorithm using a support vector machine or a naive Bayes prediction method was evaluated against the traditional method for selecting features relevant for splice site prediction. Our results show that this wrapper approach selects features that improve the performance against the use of all features and against the use of the features selected by the traditional method.

Availability: The data and additional interactive graphs on the selected feature subsets are available at http://www.psb.rug.ac.be/gps

Contact: svgro{at}gengenp.rug.ac.be yvdp{at}gengenp.rug.ac.be


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