Title: Predicting vertebrate promoters using heterogeneous clusters

Authors: Fang-Yie Leu, Lun-Ni Yang, Neng-Wen Lo, I-Long Lin

Addresses: Department of Computer Science, Tunghai University, 40799, Taiwan. ' Department of Computer Science, Tunghai University, 40799, Taiwan. ' Department of Animal Science and Biotechnology, Tunghai University, 40799, Taiwan. ' Department of Information Management, Central Police University, 33304, Taiwan

Abstract: This paper proposes a system, named the Vertebrate Promoter Prediction System (VePPS), which employs a new statistics-based approach to predict vertebrate promoters, and analyses a putative promoter sequence by investigating the presence of short promoter-specific sequences and known transcription factor binding sites. In comparison with other prediction programmes, our VePPS outperformed, e.g., promoter 2.0, by 38.0% and 12.7% in predicting promoter and non-promoter sequences, respectively.

Keywords: bioinformatics; cluster computing; k-gram; promoter prediction; performance improvement; vertebrate promoters; clustering database; transcription factor; binding site; transcription start site; heterogeneous clusters.

DOI: 10.1504/IJAHUC.2010.035534

International Journal of Ad Hoc and Ubiquitous Computing, 2010 Vol.6 No.4, pp.216 - 234

Published online: 30 Sep 2010 *

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