[Biojava-l] Short names for Amino acid symbols

[Peter Robinson]

George Waldon 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
>
>   

Thanks George, I got things working using the code in
http://biojava.org/wiki/BioJava:Cookbook:Translation:OneLetterAmbi
which is equivalent to the above.
-Peter


>> -----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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