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.
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Acknowledgments
This work was partly supported by the National Science Council in Taiwan under grants NSC98-2622-E-151-024-CC3, NSC98-2622-E-151-001-CC2, NSC98-2221-E-151-040, NSC97-2311-B-037-003-MY3, and by the grants KMU-EM-99-1.4 and DOH 100-TD-C-111-002 Dr. Hsueh-Wei Chang from the Department of Health, Taiwan.
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Yang, CH., Cheng, YH., Chuang, LY., Chang, HW. (2011). A Combined Bisulfite Restriction Analysis Bioinformatics Tool: Methyl-Typing. In: Tollefsbol, T. (eds) Epigenetics Protocols. Methods in Molecular Biology, vol 791. Humana Press. https://doi.org/10.1007/978-1-61779-316-5_6
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DOI: https://doi.org/10.1007/978-1-61779-316-5_6
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