[Biojava-l] single letter code from protein ambiguities?

Mark Schreiber markjschreiber at gmail.com
Wed May 7 10:54:49 UTC 2008

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

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

- Mark

On Wed, May 7, 2008 at 6:31 PM, community at struck.lu <community at struck.lu> 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 &quot;N&quot;, so the protein translation would
> also contain ambiguities:SymbolList symL =
> DNATools.createDNA(&quot;atnatg&quot;);SymbolList symL2 =
> DNATools.toProtein(symL);Iterator symIt =
> symL2.iterator();System.out.println(symL2.seqString());OUTPUT:XMSymbol
> hm;while (symIt.hasNext()) {&nbsp;&nbsp;&nbsp; hm = (Symbol)
> symIt.next();&nbsp;&nbsp;&nbsp; System.out.println(hm.getName());}OUTOUT:[MET
> ILE]METWould it be possible to ouput:MIMRegards,Daniel Struck
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