Methyl-Typing: an improved and visualized COBRA software for epigenomic studies.
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.
Yang
Cheng-Hong
CH
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan.
Chuang
Li-Yeh
LY
Cheng
Yu-Huei
YH
Gu
De-Leung
DL
Chen
Chung-Ho
CH
Chang
Hsueh-Wei
HW
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*
D013447:Sulfites; D004247:DNA; D004262:DNA Restriction Enzymes