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On the optimal window shape for genomic signal processing

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...

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Main Author: Gunawan, Teddy Surya
Format: Conference or Workshop Item
Language:English
Published: 2008
Subjects:
TK Electrical engineering. Electronics Nuclear engineering
Online Access:http://irep.iium.edu.my/2340/1/On_the_Optimal_Window_Shape_for_Genomic.pdf
http://irep.iium.edu.my/2340/
http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4580606&tag=1
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spelling my.iium.irep.23402012-11-06T03:12:40Z http://irep.iium.edu.my/2340/ On the optimal window shape for genomic signal processing Gunawan, Teddy Surya TK Electrical engineering. Electronics Nuclear engineering 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. 2008-05 Conference or Workshop Item REM application/pdf en http://irep.iium.edu.my/2340/1/On_the_Optimal_Window_Shape_for_Genomic.pdf 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. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4580606&tag=1
institution Universiti Islam Antarabangsa Malaysia
building IIUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider International Islamic University Malaysia
content_source IIUM Repository (IREP)
url_provider http://irep.iium.edu.my/
language English
topic TK Electrical engineering. Electronics Nuclear engineering
spellingShingle TK Electrical engineering. Electronics Nuclear engineering
Gunawan, Teddy Surya
On the optimal window shape for genomic signal processing
description 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.
format Conference or Workshop Item
author Gunawan, Teddy Surya
author_facet Gunawan, Teddy Surya
author_sort Gunawan, Teddy Surya
title On the optimal window shape for genomic signal processing
title_short On the optimal window shape for genomic signal processing
title_full On the optimal window shape for genomic signal processing
title_fullStr On the optimal window shape for genomic signal processing
title_full_unstemmed On the optimal window shape for genomic signal processing
title_sort on the optimal window shape for genomic signal processing
publishDate 2008
url http://irep.iium.edu.my/2340/1/On_the_Optimal_Window_Shape_for_Genomic.pdf
http://irep.iium.edu.my/2340/
http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4580606&tag=1
_version_ 1643604950988619776
score 13.211869

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