On Fri, Jul 10, 2009 at 10:30 AM, Peter Rice<[email protected]> wrote: > > Peter C. wrote: >> >> OK, leaving TRR aside for the moment (I'm not sure I'd have done it that >> way, but I think I follow your logic), I have some more problem cases for >> you to consider (all using the default standard NCBI table 1). >> >> Most of these are 'unambiguous ambiguous codons' as you put it, and >> I would agree using X when a more specific letter is possible isn't ideal >> but isn't actually wrong. The "ATS" and related codons (see below) >> however are simply wrong. > > They do look wrong. The "X when it could pick a residue" ones I knew of. > > The others need a closer look. The plan is to work through all possible > codons and all the NCBI genetic codes as soon as the release is out. > > It should be a simple patch to ajtranslate.c when I'm done. >
OK - I appreciate this is too last minute for the imminent EMBOSS release. >> -------------------------------------------------------------------------------------- >> >> Now for another debatable one, RAT means AAT or GAT which code >> for N and D. So, you could use B (Asx) here rather than the broader X. >> >> Similarly, you don't use J to mean leucine (L) or to isoleucine (I), and >> opt for X (again, this is justifiable). e.g. WTA > > Hmmm ... B and Z are ambiguity codes for amino acid analyser where all the > amide bonds are broken and that includes N->D and Q->E. We used to have one > of those in the lab. Similarly, J is for mass spec where I and L have the > same molecular weight. I don't consider them appropriate for translation. Well, as I said, this is debatable. On the one hand B and Z are IUPAC standards (although J isn't yet), but amino acids don't have the full ambiguous alphabet that we have for nucleotides so some might find such a translation surprising. http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html > So I plan to go for unique amino acids where possible with the ambiguity > codes. Good :) Peter C. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
