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. Copyright 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.