[Biojava-l] Short names for Amino acid symbols

[community at struck.lu]

The link should have been:

http://biojava.org/wiki/BioJava:Cookbook:Translation:OneLetterAmbi

Hope this time my webmail doesn't garble the message :-(

Greetings,
Daniel

"George Waldon" <gwaldon at geneinfinity.org> wrote:

> 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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> > http://lists.open-bio.org/mailman/listinfo/biojava-l
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