[Biojava-l] question about ambiguous symbols

[Francois Pepin]

I'd go and put all of it in, no reason that RNA should be treated
differently from DNA there.

Francois

-----Original Message-----
From: biojava-l-bounces at biojava.org
[mailto:biojava-l-bounces at biojava.org] On Behalf Of Thomas Down
Sent: 5 fevrier, 2003 12:32
To: Keith James
Cc: biojava-l at biojava.org
Subject: Re: [Biojava-l] question about ambiguous symbols


On Wed, Feb 05, 2003 at 03:52:03PM +0000, Keith James wrote:
>
> I got bitten by this too, when porting some of the code. If you look 
> in biojava-live/resources/org/biojava/bio/symbol/AlphabetManager.xml
> you will see that the default RNA alphabet contains only agcu-~. i.e. 
> no ambiguity symbols at all.
> 
> I haven't tested this, but you could hack your AlphabetManager.xml to 
> include
> 
>    <ambiguityMapping token="n">
>     <symbolref name="guanine" />
> 	<symbolref name="adenine" />
> 	<symbolref name="cytosine" />
> 	<symbolref name="uracil" />
>    </ambiguityMapping>
> 
> as in the DNA alphabet. Not sure if this is the best solution - I'm 
> sure someone will say if it's not.

Yes, I think it is the right solution.  In fact, I thought someone
checked it in last time this issue came up, but evidently not. I've
added it in CVS now.  Not sure what to do about other possible RNA
ambiguities -- does anyone use them?

     Thomas.
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