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

[mark schreiber]

> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
> Sent: Wednesday, 10 December 2003 4:52 a.m.
> To: mark schreiber
> Cc: smh1008 at cus.cam.ac.uk; taoxu at bioinformatics.ubc.ca; 
> biojava-l at biojava.org
> Subject: Re: [Biojava-l] How to create a SymbolList with a 
> String thatcontains illegal Char
> 
> 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 5.
> >
> Atomic. Our alphabets don't manage modifications well (e.g. 
> methylated DNA). Another thing to think about for v2.
> 


Hi -

It's pretty simple to add this to nucleotide and to RNA, however we get into
all sorts of trouble with making the complement table. The
SimpleReversibleTranslationTable won't tolerate RNA having a size of 5 when
DNA only has a size of 4.

I have done some investigations and inosine is complemented by 'c'. Is there
a way to make an unequal translation table for this arrangement?

If anyone has some ideas I would like to hear them but won't be able to code
them up till after Xmas as I'm off on holiday from tommorrow.

Cheers,

Mark