Optimization of MISCORE-based Motif Identification Systems
Identification of motifs in DNA sequences using classification techniques is one of computational approaches to discovering novel binding sites. In the previous work [16], we proposed a simple and effective method for motif detection using a single crisp rule governed by a mismatch-based matrix simi...
| Main Authors: | , |
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| Format: | Proceeding |
| Language: | English |
| Published: |
IEEE
2009
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/11946/ http://ir.unimas.my/id/eprint/11946/1/Optimization%20of%20MISCORE_abstract.pdf |
| _version_ | 1848837094694191104 |
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| author | Lee, Nung Kion Wang, Dianhui |
| author_facet | Lee, Nung Kion Wang, Dianhui |
| author_sort | Lee, Nung Kion |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | Identification of motifs in DNA sequences using classification techniques is one of computational approaches to discovering novel binding sites. In the previous work [16], we proposed a simple and effective method for motif detection using a single crisp rule governed by a mismatch-based matrix similarity score (MISCORE). In this paper, we consider the problem
of finding suitable motif cut-off value for MISCORE-based motif identification systems using cost-sensitivity metric. We utilize phylogenetic footprinting data to estimate the parameters in the cost function. We also extend the MISCORE to include entropy to weigh each motif model position to minimize the false positive rate. The performance evaluation is done by using artificial and real DNA sequences. The results demonstrate the feasibility and
usefulness of our proposed approach for model based cut-off
value estimation. |
| first_indexed | 2025-11-15T06:34:12Z |
| format | Proceeding |
| id | unimas-11946 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:34:12Z |
| publishDate | 2009 |
| publisher | IEEE |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-119462016-05-12T04:43:29Z http://ir.unimas.my/id/eprint/11946/ Optimization of MISCORE-based Motif Identification Systems Lee, Nung Kion Wang, Dianhui QA75 Electronic computers. Computer science T Technology (General) Identification of motifs in DNA sequences using classification techniques is one of computational approaches to discovering novel binding sites. In the previous work [16], we proposed a simple and effective method for motif detection using a single crisp rule governed by a mismatch-based matrix similarity score (MISCORE). In this paper, we consider the problem of finding suitable motif cut-off value for MISCORE-based motif identification systems using cost-sensitivity metric. We utilize phylogenetic footprinting data to estimate the parameters in the cost function. We also extend the MISCORE to include entropy to weigh each motif model position to minimize the false positive rate. The performance evaluation is done by using artificial and real DNA sequences. The results demonstrate the feasibility and usefulness of our proposed approach for model based cut-off value estimation. IEEE 2009 Proceeding NonPeerReviewed text en http://ir.unimas.my/id/eprint/11946/1/Optimization%20of%20MISCORE_abstract.pdf Lee, Nung Kion and Wang, Dianhui (2009) Optimization of MISCORE-based Motif Identification Systems. In: Bioinformatics and Biomedical Engineering, 2009. ICBBE 2009. 3rd International Conference on, 11-13 June 2009, Beijing. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5163155 10.1109/ICBBE.2009.5163155 |
| spellingShingle | QA75 Electronic computers. Computer science T Technology (General) Lee, Nung Kion Wang, Dianhui Optimization of MISCORE-based Motif Identification Systems |
| title | Optimization of MISCORE-based Motif Identification Systems |
| title_full | Optimization of MISCORE-based Motif Identification Systems |
| title_fullStr | Optimization of MISCORE-based Motif Identification Systems |
| title_full_unstemmed | Optimization of MISCORE-based Motif Identification Systems |
| title_short | Optimization of MISCORE-based Motif Identification Systems |
| title_sort | optimization of miscore-based motif identification systems |
| topic | QA75 Electronic computers. Computer science T Technology (General) |
| url | http://ir.unimas.my/id/eprint/11946/ http://ir.unimas.my/id/eprint/11946/ http://ir.unimas.my/id/eprint/11946/ http://ir.unimas.my/id/eprint/11946/1/Optimization%20of%20MISCORE_abstract.pdf |