Hi - Yes, this is absolutely possible. If biojava can create an unambigous amino acid from an ambigous codon it will. If the possible amino acids are a choice of 2 or more an ambiguity symbol (BasisSymbol) is created that contains those amino acids.
Note that if you turn any ambiguous amino acid into a String then you will just get an X so you need to decompose it into it's underlying AtomicSymbols. See http://biojava.org/wiki/BioJava:Cookbook:Alphabets:Ambiguous for some idea (except in your case you need to do the reverse). This would make another nice example for the cookbook so when you get some demo code working it would be good if you could put it up on the wiki. - Mark On Wed, May 7, 2008 at 6:31 PM, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > Hi,I am just beginning to use biojava and I have a question concerning the > parsing of protein sequences containing ambiguities:Is it possible to get all > the possible amino acids at each position of the protein sequence with a > single letter code instead of the three letter code?Suppose I would translate > a DNA sequence containing an "N", so the protein translation would > also contain ambiguities:SymbolList symL = > DNATools.createDNA("atnatg");SymbolList symL2 = > DNATools.toProtein(symL);Iterator symIt = > symL2.iterator();System.out.println(symL2.seqString());OUTPUT:XMSymbol > hm;while (symIt.hasNext()) { hm = (Symbol) > symIt.next(); System.out.println(hm.getName());}OUTOUT:[MET > ILE]METWould it be possible to ouput:MIMRegards,Daniel Struck > _________________________________________________________ > Mail sent using root eSolutions Webmailer - www.root.lu > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
