Standard letter for 5-methylcytosine I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base. At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U. Is there a standard letter for 5-methylcytosine? The only example I've found is this paper, which uses an italic _C_ for 5mc, but I want a distinct letter. The three candidates I've thought of are: * **5** \- for '5-methylcytosine' * **M** \- for 'methyl' * **B** \- Since methylation of **U** gives you **T** , which is one place earlier in the alphabet, so methylation of **C** gives **B**.

Well, don't use **M** or **B** , those are already taken ( **C** or **A** , and **not A** , respectively). You can see the full list here: < (The enWiki article on Nucleobases lists a few others but I would ignore those as 1. D is present in both and 2. they are rare and inapplicable)

5-methylcytosine isn't on there. If you want to be pedantic about it, 5-methylcytosine is an epigenetic marker and as such is by definition _not_ a genetic sequence; that remains simply a C and, genetically, the _sequence_ is the same, despite the fact that it may indeed make a difference.

Most of the time people use m5C, so I'd go with **5** if I were you. That certainly isn't used for anything else and if you must use a single character most anybody will know what you are talking about.