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.
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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.
So I plan to go for unique amino acids where possible with the ambiguity codes.
What do our users think?
regards,
Peter
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