Surprisingly there is not a method ro reverseTranslation in RNATools, I
might add one. It does however give a nice opportunity to see how biojava
translates symbols from one Alphabet to another.
You would do it like this:
public static SymbolList rt(SymbolList rna)
throws IllegalSymbolException, IllegalAlphabetException{
ReversibleTranslationTable rtt = RNATools.transcriptionTable();
Symbol[] syms = new Symbol[rna.length()];
//reverse RNA
rna = SymbolListViews.reverse(rna);
for(int i = 1; i <= rna.length(); i++){
syms[i-1] = rtt.untranslate(rna.symbolAt(i));
}
SymbolListFactory fact = new SimpleSymbolListFactory();
SymbolList dna = fact.makeSymbolList(syms, syms.length,
rtt.getSourceAlphabet());
System.out.println(dna.toString());
return dna;
}
The key interface is the ReversibleTranslationTable. TranslationTable (the
parent interface) has a method to translate a Symbol from one alpha to
another. A ReversibleTranslationTable extends this by providing a second
method to untranslate. The RNATools.transcriptionTable maps DNA to RNA.
The untranslate method does the opposite.
Anyone want to wirte that up for Biojava in Anger?
- Mark
Jacob Rohde <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
08/15/2005 04:26 PM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-l] Reverse transcription
Hi,
On 8/15/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]>
wrote:
> Take a look at http://www.biojava.org/docs/bj_in_anger/ReverseComplement.htm
>
>
>
Thanks for you replies Mark.
Yes, I've read about the reverseComplement. It may be I'm dense here,
but I can't see how it can help me go from RNA to DNA. The way I
understand reverseComplement is that it gives the complementary strand
of the argument in the reverse order (5'-3'), but in the same
alphabet.
I need to go from RNA to DNA. Again, I might be overlooking something?!?!
On 8/15/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]>
wrote:
>See also DNATools.transcribeToRNA(), especially read the >javadocs and
>contrast that with DNATools.toRNA().
Yes, I can see the difference. transcribeToRNA() assumes the argument
is the template strand in the 5'-3' direction whereas toRNA() takes
the coding strand as argument (it simply translates the alphabet
without any consideration of an actual transcription event).
/Jacob
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