Translation part #2

Going back to translation module of the project. I was wondering how many of the existing translation codes (actually they are not so different, existing codes differ usually only by couple of codons) should I implement.

I referred to NCBI page ( https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi ) to check what codes are broadly accepted and decided that I will implement all of the codes presented on the page (as many as 24):

1. The Standard Code

2. The Vertebrate Mitochondrial Code

3. The Yeast Mitochondrial Code

4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code

5. The Invertebrate Mitochondrial Code

6. The Ciliate, Dasycladacean and Hexamita Nuclear Code

7. The Echinoderm and Flatworm Mitochondrial Code

8. The Euplotid Nuclear Code

9. The Bacterial, Archaeal and Plant Plastid Code

10. The Alternative Yeast Nuclear Code

11. The Ascidian Mitochondrial Code

12. The Alternative Flatworm Mitochondrial Code

13. Chlorophycean Mitochondrial Code

14. Trematode Mitochondrial Code

15. Scenedesmus obliquus Mitochondrial Code

16. Thraustochytrium Mitochondrial Code

17. Pterobranchia Mitochondrial Code

18. Candidate Division SR1 and Gracilibacteria Code

19. Pachysolen tannophilus Nuclear Code

20. Karyorelict Nuclear

21. Condylostoma Nuclear

22. Mesodinium Nuclear

23. Peritrich Nuclear

24. Blastocrithidia Nuclear

The question that remains is whether to include all alternative start (initiation) codons and how to annotate the results to make it clear for the user. This is even more important how to mark the translation starts/stops, alternative starts. User experience – part #1 I guess.

So translation module is not finished yet.