althonos / althonos/pyrodigal

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

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enhancement
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Description

A [recent study](https://www.science.org/doi/10.1126/science.adu2404) 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.

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