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Bioinformatics Vol. 18 no. 90002 2002
Pages S27-S34
© 2002 Oxford University Press

Modeling splicing sites with pairwise correlations

Masanori Arita 1, Koji Tsuda 1 and Kiyoshi Asai 1

1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan

Received on April 8, 2002 ; accepted on June 15, 2002

Motivation: A new method for finding subtle patterns in sequences is introduced. It approximates the multiple correlations among residuals with pair-wise correlations, with the learning cost O(m2n) where n is the number of training sequences, each of length m. The method suits to model splicing sites in human DNA, which are reported to have higher-order dependencies.

Results: By computational experiments, the prediction accuracy of our model was shown to surpass that of previously reported Markov models for the prediction of acceptor sites in human.

Availability: The C++ source code is available on request from the authors.

Contact: m-arita{at}aist.go.jp


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