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Related Experiment Video

Updated: Jun 17, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

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

Cheng-Hong Yang1, Li-Yeh Chuang, Yu-Huei Cheng

  • 1Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan.

FEBS Letters
|December 23, 2009
PubMed
Summary

Methyl-Typing software expands the utility of Combined Bisulfite Restriction Analysis (COBRA) by enabling restriction enzyme mining for DNA methylation analysis. This tool aids in identifying more restriction enzymes for COBRA, enhancing methylation quantification capabilities.

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Last Updated: Jun 17, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

DNA Methylation: Bisulphite Modification and Analysis
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Targeted DNA Methylation Analysis by Next-generation Sequencing
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Targeted DNA Methylation Analysis by Next-generation Sequencing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Epigenetics

Background:

  • Combined bisulfite restriction analysis (COBRA) is a widely used method for DNA methylation quantification.
  • The current COBRA method is limited by the availability of suitable restriction enzymes for analysis.

Purpose of the Study:

  • To introduce Methyl-Typing, a novel web-based software for comprehensive restriction enzyme mining.
  • To facilitate the identification of new restriction enzymes for enhanced COBRA applications.

Main Methods:

  • Development of a web-based tool, Methyl-Typing, for analyzing bisulfite-converted sequences.
  • Inclusion of features for gene information, sequence retrieval, PCR primer design, and promoter analysis.
  • Mining of restriction enzymes targeting CpG and GpC sites within promoter regions.

Main Results:

  • Methyl-Typing successfully identifies restriction enzyme recognition sites in methyl-cytosine-containing sequences.
  • Experimental validation confirmed the utility of four representative enzymes identified by the tool using COBRA.
  • The software provides comprehensive data for COBRA-restriction enzyme mining.

Conclusions:

  • Methyl-Typing significantly expands the scope of COBRA by providing a robust platform for restriction enzyme discovery.
  • This tool enhances the capacity for DNA methylation quantification and epigenetic research.
  • Methyl-Typing is freely accessible online, promoting wider adoption in the scientific community.