On the optimal window shape for genomic signal processing

Gunawan, Teddy Surya (2008) On the optimal window shape for genomic signal processing. In: International Conference on Computer and Communication Engineering (ICCCE 2008), 13-15 May 2008, Kuala Lumpur.

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Abstract

The segments of DNA molecule, called genes are known to carry useful information in their protein coding regions (exons) and are responsible for protein synthesis. The most popular frequency domain technique for gene identification is by using a sliding window DFT technique to locate the well known period-3 property in DNA sequences. This paper investigates the use of parametric and nonparametric window types with DFT based period-3 detection method to identify the coding and noncoding regions. The HMR195 dataset was selected for the performance comparison utilizing the receiver operating characteristic (ROC) curve and area under ROC (AUC) measure. Results showed that the Bartlett window (nonparametric) and Gaussian window with alpha=2.2401 (parametric) provide the optimal window shape compared to 13 other window types for gene identification of coding and noncoding regions.

Item Type:	Conference or Workshop Item (Full Paper)
Additional Information:	5588/2340 (Print ISBN: 9781424416912, DOI: 10.1109/ICCCE.2008.4580606)
Uncontrolled Keywords:	biology computing , discrete Fourier transforms , frequency-domain analysis , genetics , molecular biophysics , proteins , sequences , signal processing
Subjects:	T Technology > TK Electrical engineering. Electronics Nuclear engineering
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Engineering > Department of Electrical and Computer Engineering
Depositing User:	Prof. Dr. Teddy Surya Gunawan
Date Deposited:	05 Nov 2012 15:21
Last Modified:	06 Nov 2012 11:12
URI:	http://irep.iium.edu.my/id/eprint/2340

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