title: Methyl-Typing: an improved and visualized COBRA software for epigenomic studies.
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.
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan.
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: De-Leung
authors.initials: DL
authors.lastname: Gu
authors.forename: Chung-Ho
authors.initials: CH
authors.lastname: Chen
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; D004247:DNA; D004262:DNA Restriction Enzymes