Methyl-Typing: An improved and visualized COBRA software for epigenomic studies

Yang, Cheng-Hong; Chuang, Li-Yeh; Cheng, Yu-Huei; Gu, De-Leung; Chen, Chung-Ho; Chang, Hsueh-Wei

doi:10.1016/j.febslet.2009.12.026

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Volume 584, Issue 4 , Pages 739-744, 19 February 2010

Methyl-Typing: An improved and visualized COBRA software for epigenomic studies

Edited by Paul Bertone

Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
- Department of Network Systems, Toko University, Chiayi, Taiwan
Li-Yeh Chuang
- Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
- Corresponding authors. Address: Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan (H.-W. Chang). Fax: +886 7 312 5339.
Yu-Huei Cheng
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
De-Leung Gu
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
Chung-Ho Chen
- Department of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Oral and Maxillofacial Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Corresponding authors. Address: Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan (H.-W. Chang). Fax: +886 7 312 5339.

Received 14 October 2009; received in revised form 14 December 2009; accepted 16 December 2009. published online 22 December 2009.

Abstract

Combined bisulfite restriction analysis (COBRA) is one of the most commonly used methylation quantification methods. However, it focuses on relatively few restriction enzymes. Here, we present Methyl-Typing, a web-based software that provides restriction enzyme mining data for methyl-cytosine-containing sequences following bisulfite-conversion. Gene names, accession numbers, sequences, PCR primers, and file upload are accessible for input. Promoter sequences and restriction enzymes for CpG- and GpC-containing recognition sites are retrieved. Four representative enzymes were tested successfully by COBRA on the experimental work. Therefore, the Methyl-Typing tool provides a comprehensive COBRA-restriction enzyme mining. It is freely available at http://bio.kuas.edu.tw/methyl-typing.

Abbreviations: COBRA, combined bisulfite restriction analysis, CTCF, CCCTC-binding factor, CTCFBSDB, CCCTC-binding factor-binding site database, RFLP, random fragment length polymorphism

Keywords: Methylation, COBRA, Restriction enzyme, Software, Promoter