title: A combined bisulfite restriction analysis bioinformatics tool: methyl-typing.
abstract: In this chapter, we introduce our developed freeware tool Methyl-Typing. It provides methylation-related bioinformatics with a special focus on combined bisulfite restriction analysis (COBRA). We give an overview of the implementation and program modules for Methyl-Typing. Various databases and methylation-related functions are integrated into Methyl-Typing and a helpful example is illustrated in detail. Several input protocols and their outputs for COBRA-related information are demonstrated, such as the inputs of multiple gene names in official gene symbols, multiple accession numbers for nucleotide sequence retrieval, multiple template sequences in a free format, primer sequences, and file uploads. The program goal of Methyl-Typing is to provide computation and visualization of the essential information for COBRA assay so that methylation can easily be analyzed by COBRA. It is a fast and efficient tool for providing all possible methylation sites of restriction enzymes.
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: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D019295:Computational Biology / Q000379:methods*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000187:drug effects / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D057225:Data Mining; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D051379:Mice; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012097:Repressor Proteins / Q000378:metabolism; D015183:Restriction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software; D013447:Sulfites / Q000494:pharmacology*; D018511:Systems Integration
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C000619698:Ctcf protein, mouse; D017931:DNA Primers; D012097:Repressor Proteins; D013447:Sulfites; C042345:hydrogen sulfite