Atomic. Our alphabets don't manage modifications well (e.g. methylated DNA). Another thing to think about for v2.Is 'i' actually a legal symbol from the RNA alphabet, in terms of biojava? If not how should we define it? Would it be best modelled as an atomic symbol or some kind of ambiguity? Stretching back to my biochem undergrad days I think it should be atomic. That will mean the RNA Alphabets size is 5.
Both I guess. Defninitely should be in RNA.
I've just checked the AlphabetManager.xml and inosine isn't in there. If there are no objections I will add it as an AtomicSymbol tommorrow with a mapping to the character 'i'. The question is should it be added as a member of the RNA alphabet or as a member of the nucleotide alphabet or both?
Matthew
- Mark
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