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Beyond Bioinformatics | |
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Title |
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CpGIF: an algorithm for the identification of CpG islands
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Authors |
Sujuan Ye1, Asai Asaithambi1 and Yunkai Liu1,*
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Affiliation |
1Department of Computer Science, University of South Dakota, Vermillion, SD, USA
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Yunkai.Liu@usd.edu; * Corresponding author
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Article Type |
Prediction Model
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Date |
received May 01, 2008; revised May 13, 2008; accepted May 15, 2008; published May 20, 2008
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Abstract |
CpG islands (CGIs) play a fundamental role in genome analysis and annotation, and contribute to improving the accuracy of promoter prediction. Besides, CGIs in promoter regions are abnormally methylated in cancer cells and thus can be used as tumor markers. However, current methods for identifying CGIs suffer from various drawbacks. We present a new algorithm for detecting CGIs, called CpG Island Finder (CpGIF), which combines the best features in the most commonly used algorithms and avoids their disadvantages as much as possible. Five public tools for CpG island searching are used to compare with CpGIF for the assessment of accuracy and computational efficiency. The results reveal that CpGIF has higher performance coefficient and correlation coefficient than these previous methods, which indicates that CpGIF is able to provide high sensitivity and specificity at the same time. CpGIF is also faster than those methods with comparable prediction accuracy.
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Keywords |
CpG islands; CpG dinucleotides; clustering algorithm
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Citation |
Ye et al., Bioinformation 2(8): 335-338 (2008)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Agreement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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