UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery

Authors:
Jianxin Wang;De Yang
Affiliations:
School of Information Science and Engineering, Central South University, Changsha, 410083, PR China.;School of Information Science and Engineering, Central South University, Changsha, 410083, PR China
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2008

Citing 3
Cited 0

Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization

Machine Learning - Special issue on applications in molecular biology
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
A Uniform Projection Method for Motif Discovery in DNA Sequences

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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Abstract

Motif discovery is a significant problem in Bioinformatics. According to the complexity of most signals in biologic sequences, there are no extremely good models or dependable algorithms to solve this problem. This paper introduces the Uniform Projection and Neighbourhood Thresholding (UPNT) algorithm, which is based on two efficient strategies: Uniform Projection and Neighbourhood-based Thresholding. In the UPNT algorithm, the policy of uniform projection leads to fewer projections, while the strategy of refining the buckets after aggregation results in great abatement of the number of buckets to be refined. This paper further demonstrates its superiority over other projection algorithms by the experiments.