The link http://biojava.org/wiki/BioJava:Cookbook:Translation:OneLetterAmbiDaniel does not seem to work.
Did you try SymbolTonenization? Something like: Symbol s; SymbolTokenization tok= ProteinTools.getTAlphabet().getTokenization("token"); String s = tok.tokenizeSymbol(s); Should give you the short name of any given symbol. - George > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:biojava-l- > [EMAIL PROTECTED] On Behalf Of Peter Robinson > Sent: Sunday, July 27, 2008 8:57 AM > To: biojava-l@lists.open-bio.org > Subject: [Biojava-l] Short names for Amino acid symbols > > Hi, > > thanks to all on the list who helped me get started with Biojava, and by > the way, the online documents are quite helpful! > > I am trying to develop some code to look for signs of positive selection > in human sequences by making multiple alignments of protein sequences > and mapping the nucleotide sequences onto this alignment and checking > synonymous and nonsynonymous nucleotide substitutions in several species > (etc). > > A few small questions; > 1) I have written a class to encapsulate all I need from a given Genbank > mRNA sequence; the entire mRNA, the CDS and the corresponding protein > sequence. I have some methods such as the following: > > private void setCDSSequence() { > Feature CDS = getCDSFeature(this.completeSequence); > Location loc = CDS.getLocation(); > SymbolList symL = this.completeSequence.subList(loc.getMin(), > loc.getMax()-3); //-3 to remove stop codon > this.CDS= symL; > } > > Question: Why is there (seemingly) no way in Biojava to create a > Sequence object instead of a SymbolList object? Or did I miss something? > > 2) I would then like to printout the protein alignment to check for > correctness, and it seems there is no way of getting from a symbol to > the one-letter aminoacid code. That is, > > proteinAlignment.get(j).symbolAt(k).getName() > > will return "Ala" instead of "A" etc. Is there a good way of getting the > short symbols? > > Thanks, Peter > _______________________________________________ > 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