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Bioinformatics Vol. 16 no. 2 2000
Pages 152-158
© 2000 Oxford University Press

Modeling splice sites with Bayes networks

Deyou Cai 1, Arthur Delcher 2, Ben Kao 1 and Simon Kasif 1

1 Department of Electrical Engineering and Computer Science, University of Illinois, Chicago, IL 60607, USA
2 Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA andCelera Genomics, Rockville, MD 20850, USA

Motivation: The main goal in this paper is to develop accurate probabilistic models for important functional regions in DNA sequences (e.g. splice junctions that signal the beginning and end of transcription in human DNA). These methods can subsequently be utilized to improve the performance of gene-finding systems. The models built here attempt to model long-distance dependencies between non-adjacent bases.

Results: An efficient modeling method is described which models biological data more accurately than a first-order Markov model without increasing the number of parameters. Intuitively, a small number of parameters helps a learning system to avoid overfitting. Several experiments with the model are presented, which show a small improvement in the average accuracy as compared with a simple Markov model. These experiments suggest that single long distance dependencies do not help the recognition problem, thus confirming several previous studies which have used more heuristic modeling techniques.

Availability: This software is available for download and as a web resource at http://www.ai.uic.edu/software

Contact: kasif{at}eecs.uic.edu

Received on November 6, 1998 ; revised on April 23, 1999 ; accepted on June 17, 1999

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