Incorporating a pyrrolysine-encoding translation table (34) into pyrodigal

[apcamargo]

A recent study reported that some Archaea use a previously uncharacterized genetic code to incorporate pyrrolysine (Pyl) at TAG codons. Integrating this new translation table (referred to as "34" in the paper) into pyrodigal, along with a pre-trained model for Methanococcoides alvi/burtonii in metagenome mode, should be straightforward. However, it is unclear how to represent the resulting protein sequences, as pyrrolysine’s one-letter code ("O") is not part of the standard amino acid set.

@althonos do you have any thoughts on this? I could prepare a PR for this.

[althonos]

Hi @apcamargo ! That sounds good and pretty straightforward indeed. I think for consistency I would propose to do the following:

• Incorporate the Pyl / TAG codon in the main Pyrodigal library, so that it can now be used to in single mode
• Add an external library (like pyrodigal-gv and the more recent pyrodigal-rv), e.g. pyrodigal-archaea with the new pre-trained metagenomic model.

The reason I think this is better rather than immediately integrating with Pyrodigal is that I think it's better if the new metagenomic model is opt-in, otherwise this may cause some predictions to become inconsistent between Pyrodigal versions (albeit more correct if the new predictions are made with the M. alvi/burtonii model).

Does that sound reasonable or is there a reason to have it in "stock" Pyrodigal?

In any case I'd be happy with a PR 😄 Cheers!