I'd go and put all of it in, no reason that RNA should be treated differently from DNA there.
Francois -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] On Behalf Of Thomas Down Sent: 5 fevrier, 2003 12:32 To: Keith James Cc: [EMAIL PROTECTED] 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. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
