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Implementation of a Classification-Based Prediction Model for Plant mRNA Poly(A)Sites

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The poly(A) site of a messenger RNA (mRNA) defines the end of a transcript during eukaryotic gene expression. Finding poly(A) sites in genome sequences can help to annotate the ends of genes and predict alternative polyadenylation. However, it is challenging to predict plant poly(A) sites using computational methods because of the weak signals that determine the poly(A) sites. Here we describe a classification based plant poly(A) site recognition model. First, several feature representation methods like factorial moments, M encoding, and weight of signal patterns are adopted to describe the makeup of nucleotide sequences of poly(A) signals. Then, a training and testing model using Bayesian network as the classification algorithm are built to predict plant poly(A) sites. Comparing to previous plant poly(A) sites prediction software PASS that we developed and three other models concerned about human or animal data, the recognition model introduced here shows good performance, flexibility and expansibility.
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Keywords: NUCLEOTIDE SEQUENCES; POLYADENYLATION; RNA

Document Type: Research Article

Publication date: May 1, 2010

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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