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

mark schreiber markjschreiber at hotmail.com
Wed Dec 10 04:20:18 EST 2003


-----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
OK so the vote is for Atomic. At this stage I'm not going to add it to any
translation tables as my biochem is not up to figuring out what effect
inosine has on a codon.

- Mark

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.

>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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