When converting a DNA strand to an RNA strand, RNATools has a hardcoded T -> U and returns the symbol otherwise. This breaks if an ambiguous nucleotide is passed in, since they don't trip the T check. I looked in the alphabet XML file, and there are no ambiguous RNA symbols.
The use case I'm facing is translating a DNA sequence. The translation in BioJava goes through an RNA sequence, so ambiguous residues foul it up. So, I propose one of the following solutions: * Introduce ambiguous RNA symbols that are analogous to the DNA symbols. * Introduce one ambiguous RNA symbol that all ambigous DNA symbols map to. * Break the biological parallel and translate DNA directly to amino acids. If I don't hear from anyone, I'll do the third. Greg _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
