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Dept Comp Sci & Comp Eng
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La Trobe University
Victoria 3086
AUSTRALIA
Tel: +61 3 9479 1107
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Research Publications - Abstract
Department of Computer Science & Computer Engineering
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Wang, D., and Lee, N.K. |
| Publication Year: |
2009 |
| Paper Title: |
Optimization of MISCORE-based Motif Identification Systems |
| Conference Name: |
The 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2009) |
| Venue: |
Beijing, China |
| Volume: |
iCBBE 2009 |
| Pages: |
1 - 4 |
| Abstract: |
Identification of motifs in DNA sequences using classification techniques is one of computational approachesto discovering novel binding sites. In the previous work [16], 23 proposed a simple and effective method for motif detection using a single crisp rule governed by a mismatch-based matrix cimilarity 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 miminize the false positive rate. The perfomance 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.
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