BioJava:Cookbook:Translation:Single
How do I translate a single codon to a single amino acid?
The general translation example shows how to use RNATools to translate a RNA SymbolList into a Protein SymbolList but most of what goes on is hidden behind the convenience method translate(). If you only want to translate a single codon into a single amino acid you get exposed to a bit more of the gory detail but you also get a chance to figure out more of what is going on under the hood.
There are actually a number of ways to do this, below I have presented only one.
```java import org.biojava.bio.seq.*; import org.biojava.bio.symbol.*;
public class SingleTranslationDemo {
public static void main(String[] args) {
//make a compound alphabet where codons are Symbols
Alphabet a = AlphabetManager.alphabetForName("(RNA x RNA x RNA)");
//get our translation table using one of the static names from TranslationTable
TranslationTable table = RNATools.getGeneticCode(TranslationTable.UNIVERSAL);
try {
//make a 'codon'
SymbolList codon = RNATools.createRNA("UUG");
//get the representation of that codon as a Symbol
Symbol sym = a.getSymbol(codon.toList());
//translate to amino acid
Symbol aminoAcid = table.translate(sym);
/*
* This bit is not required for the translation it just proves that the
* Symbol is from the right Alphabet. An Exception will be thrown if it
* isn't.
*/
ProteinTools.getTAlphabet().validate(aminoAcid);
//i think it is Leucine
System.out.println(aminoAcid.getName());
}
catch (IllegalSymbolException ex) {
ex.printStackTrace();
}
}
} ```