Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/36356
Title: An exploration of the triplet periodicity in nucleotide sequences with a mature self-adaptive spectral rotation approach
Authors: Chen, B
Ji, P 
Issue Date: 2014
Publisher: Hindawi Publishing Corporation
Source: Journal of applied mathematics, 2014, 176943 How to cite?
Journal: Journal of applied mathematics 
Abstract: Previously, for predicting coding regions in nucleotide sequences, a self-adaptive spectral rotation (SASR) method has been developed, based on a universal statistical feature of the coding regions, named triplet periodicity (TP). It outputs a random walk, that is, TP walk, in the complex plane for the query sequence. Each step in the walk is corresponding to a position in the sequence and generated from a long-termstatistic of the TP in the sequence. The coding regions (TP intensive) are then visually discriminated from the noncoding ones (without TP), in the TP walk. In this paper, the behaviors of the walks for random nucleotide sequences are further investigated qualitatively. A slightly leftward trend (a negative noise) in such walks is observed, which is not reported in the previous SASR literatures. An improved SASR, named the mature SASR, is proposed, in order to eliminate the noise and correct the TP walks. Furthermore, a potential sequence pattern opposite to the TP persistent pattern, that is, the TP antipersistent pattern, is explored. The applications of the algorithms on simulated datasets show their capabilities in detecting such a potential sequence pattern.
URI: http://hdl.handle.net/10397/36356
ISSN: 1110-757X (print)
DOI: 10.1155/2014/176943
Rights: Copyright © 2014 Bo Chen and Ping Ji. 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.
The following article: Chen, B., & Ji, P. (2014). An exploration of the triplet periodicity in nucleotide sequences with a mature self-adaptive spectral rotation approach. Journal of applied mathematics, 2014, is available at https//doi.org/10.1155/2014/176943
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