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An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach
Joint Authors
Source
Journal of Applied Mathematics
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-08-12
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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-term statistic 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.
American Psychological Association (APA)
Chen, Bo& Ji, Ping. 2014. An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach. Journal of Applied Mathematics،Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-452098
Modern Language Association (MLA)
Chen, Bo& Ji, Ping. An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach. Journal of Applied Mathematics No. 2014 (2014), pp.1-9.
https://search.emarefa.net/detail/BIM-452098
American Medical Association (AMA)
Chen, Bo& Ji, Ping. An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach. Journal of Applied Mathematics. 2014. Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-452098
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-452098