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Title |
MethFinder - A software package for prediction of human tissue-specific methylation status of CpG islands |
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Authors |
Priyanka James$, Reshmi Girijadevi$, Sona Charles & M Radhakrishna Pillai* |
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Affiliation |
Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala-695014, India.
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mrpillai@rgcb.res.in; *Corresponding author
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Article Type |
Software |
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Date |
Received December 06, 2012; Accepted December 10, 2012; Published January 09, 2013
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Abstract |
DNA methylation, the highly studied epigenetic mechanism which is involved in the regulatory events of various cellular processes like chromatin structure modifications, chromosomal inactivation, gene expressional patterns, embriyonic developments and transcriptional modification etc. Various high throughput techniques evolved for direct detection of methylation actions as well as information across the entire region. However, despite high throughput technological advances in experimental field, the development of software tools that has been dedicated to the prediction of epigenetic information from specific genome sequences is warranted. To this end we developed a tissue specific classifier MethFinder based on the frequency of novel sequence patterns across nine human tissues that was capable of discriminating methylation prone and methylation resistant CpG islands with an overall accuracy of 93%.
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Availability |
MethFinder is freely available at www.rgcb.res.in/methfinder
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Keywords |
DNA methylation, CpG islands, Support Vector Machines (SVM).
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Citation |
James et al.
Bioinformation 9(1): 061-064 (2013) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |