[Biojava-l] Short names for Amino acid symbols

[community at struck.lu]

The link should have
been:http://biojava.org/wiki/BioJava:Cookbook:Translation:OneLetterAmbiHope
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 > > _______________________________________________ > >
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org > >
http://lists.open-bio.org/mailman/listinfo/biojava-l >
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