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...
| Main Author: | |
|---|---|
| Format: | Proceeding Paper |
| Language: | English |
| Published: |
2008
|
| Subjects: | |
| Online Access: | http://irep.iium.edu.my/2340/ http://irep.iium.edu.my/2340/1/On_the_Optimal_Window_Shape_for_Genomic.pdf |
| _version_ | 1848775992473026560 |
|---|---|
| author | Gunawan, Teddy Surya |
| author_facet | Gunawan, Teddy Surya |
| author_sort | Gunawan, Teddy Surya |
| building | IIUM Repository |
| collection | Online Access |
| 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. |
| first_indexed | 2025-11-14T14:23:00Z |
| format | Proceeding Paper |
| id | iium-2340 |
| institution | International Islamic University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T14:23:00Z |
| publishDate | 2008 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | iium-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 Proceeding Paper PeerReviewed 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 |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Gunawan, Teddy Surya On the optimal window shape for genomic signal processing |
| title | 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_short | On the optimal window shape for genomic signal processing |
| title_sort | on the optimal window shape for genomic signal processing |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://irep.iium.edu.my/2340/ http://irep.iium.edu.my/2340/ http://irep.iium.edu.my/2340/1/On_the_Optimal_Window_Shape_for_Genomic.pdf |