I know that this discussion has come up before and it seems that people generally agreed that it would be OK to add X to the dna ambiguity symbol list. I certainly need it in my work because I deal with sequence files generated by other programs that use X.
In the old IO model is was easy enough to modify the AlphabetManager.xml file so I did and have not worried about it for months. Well with the new model it is not so easy. As best I can tell there can only exist one ambiguity symbol for and set of bases. So you can not have both n and x act as symbols for AGCT. So if you add x as agct n will no longer work. If you add x as agc, v will no longer work (last one in the XML file wins). I'm guessing that there is a Map somewhere, though I have not found it. I have temporarily gotten around it by just wiping out my 'b'. Since I really don't worry about ambiguity in my DNA much but must be able to read X. But does anyone see a proper solution that would give let us use X? David _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
