Default codon tables

[Koeng101]

We should add default codon tables of the following organisms:

1. Escherichia coli MG1655
2. Bacillus subtilis 168
3. Vibrio natriegens (whatever type strain)
4. Saccharomyces cerevisiae BY4741/BY4742 (used for knockdown collections)
5. Yarrowia lipolytica (apparently used quite a bit in production, use type strain)
6. Pichia pastoris NRRL Y-7556
7. Kluyveromyces marxianus NRRL Y-6860 (it zoom speed yeast)
8. Homo sapiens (kinda yucky)

[isaacguerreir]

I think we will have only the Bacillus Subtilis 168 codon table easy available. The other ones will be probably created by taking the proteins from the genome of each specie/strain.

Do you guys suggest using some specific genome for each organism?

[Koeng101]

Just the type strain genomes. I've suggested a few of them above.

[rkrishnasanka]

@Koeng101 you mean something like this package ?

https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/python_codon_tables

[Koeng101]

Close, but not quite! They pull from http://www.kazusa.or.jp/codon/ , which is woefully out of date (last updated 2007), and sometimes, just plain wrong. The files are also not static but pulled every time from the codon usage database, requiring network access to use the program.

[Koeng101]

Depends on #313, so deprioritizing for now and upping priority there

[github-actions]

This issue has had no activity in the past 2 months. Marking as stale.