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The Scientific World Journal
Volume 2014, Article ID 327306, 14 pages
http://dx.doi.org/10.1155/2014/327306
Research Article

Rule-Based Knowledge Acquisition Method for Promoter Prediction in Human and Drosophila Species

1Department of Management Information System, Asia Pacific Institute of Creativity, Miaoli 351, Taiwan
2School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
3Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
4Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan

Received 31 August 2013; Accepted 10 October 2013; Published 29 January 2014

Academic Editors: L. Bao and J. Wang

Copyright © 2014 Wen-Lin Huang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The rapid and reliable identification of promoter regions is important when the number of genomes to be sequenced is increasing very speedily. Various methods have been developed but few methods investigate the effectiveness of sequence-based features in promoter prediction. This study proposes a knowledge acquisition method (named PromHD) based on if-then rules for promoter prediction in human and Drosophila species. PromHD utilizes an effective feature-mining algorithm and a reference feature set of 167 DNA sequence descriptors (DNASDs), comprising three descriptors of physicochemical properties (absorption maxima, molecular weight, and molar absorption coefficient), 128 top-ranked descriptors of 4-mer motifs, and 36 global sequence descriptors. PromHD identifies two feature subsets with 99 and 74 DNASDs and yields test accuracies of 96.4% and 97.5% in human and Drosophila species, respectively. Based on the 99- and 74-dimensional feature vectors, PromHD generates several if-then rules by using the decision tree mechanism for promoter prediction. The top-ranked informative rules with high certainty grades reveal that the global sequence descriptor, the length of nucleotide A at the first position of the sequence, and two physicochemical properties, absorption maxima and molecular weight, are effective in distinguishing promoters from non-promoters in human and Drosophila species, respectively.