Everyone, I've stepped through with a debugger, and this is a bad bug.
The code to translate from RNA->Protein does the following: - Take the ASCII Value for the 3 RNA bases, and multiple the first pos by 16, second by 4 and third by 1 and add them up. - Assume there won't be any collisions. Here are the values which it then uses: A:65 G:71 C:67 U:85 N:78 ANA: 1417 CAU: 1417 ANG: 1423 CGA: 1423 Notice any hash collisions? I don't get why this wasn't done in a standard JavaHashMap which would ensure that any collisions were resolved. This is a pretty critical bug for a biology informatics package. Nick On 20 September 2013 13:45, Nick England <[email protected]> wrote: > 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 <[email protected]> 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 >> >> ________________________________ >> >> This email and any attachments thereto may contain private, confidential, >> and privileged material for the sole use of the intended recipient. Any >> review, copying, or distribution of this email (or any attachments thereto) >> by others is strictly prohibited. If you are not the intended recipient, >> please contact the sender immediately and permanently delete the original >> and any copies of this email and any attachments thereto. >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
