[Biojava-l] issue with translating codons with N

[Nick England]

Hara,

Hmm this is rather odd. I get the same issue with that sequence with a
custom engine as well.

My code has:
Builder builder = new TranscriptionEngine.Builder();
    builder.initMet(false);
    builder.translateNCodons(true);
    builder.trimStop(false);
    TranscriptionEngine engine = builder.build();
    Sequence<AminoAcidCompound> seq=engine.translate(new
DNASequence("GTNTGTTAGTGT"));
    assertEquals("XC*C", seq.toString());
    Sequence<AminoAcidCompound> seq2=engine.translate(new
DNASequence("ANAANG"));
    System.out.println(seq2);
the first sequence translates as expected, but your sequence is translating
as HR, when it should be XX. This looks like a pretty bad bug!

Nick


On 19 September 2013 19:59, Hara Dilley <hdilley at sutrobio.com> wrote:

> Hi,
>
> Is there an issue with the DNA Translation in biojava3.core?
> It appears that it wants to translate "N" in certain cases
> Executing:
> new
> DNASequence("ANAANG").getRNASequence().getProteinSequence().getSequenceAsString();
> will produce  aa HR.
>
> thanks
> Hara
>
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