[Biojava-l] How to create a SymbolList with a String thatcontains illegal Char

Matthew Pocock matthew_pocock at yahoo.co.uk
Tue Dec 9 10:52:16 EST 2003

mark schreiber wrote:

>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
Atomic. Our alphabets don't manage modifications well (e.g. methylated 
DNA). Another thing to think about for v2.

>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?
Both I guess. Defninitely should be in RNA.


>- Mark

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