[Biojava-l] Short names for Amino acid symbols

[George Waldon]

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: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-
> bounces at lists.open-bio.org] On Behalf Of Peter Robinson
> Sent: Sunday, July 27, 2008 8:57 AM
> To: biojava-l at 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
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