Closed janas-sebastien closed 5 years ago
I now understand that it's considered as an alternative start codon, that's why it's translated in M. My issue was that the change in the behavior of the code suddenly broke our unit tests. It would have be better to implement the new behavior as an option to translate. Because now, all people who are using translate to translate a single triplet will see their code broken.
Moreover, the documentation does not say that the sequence must be a complete sequence (starting at the start codon).
Hi @janas-sebastien
You're right that adding an option would have been better. Sorry for the inconvenience.
This is now done: I just added the no.init.codon
argument to translate()
(https://github.com/Bioconductor/Biostrings/commit/dcd915c21b96d4d981d4530f913ff9108239e129) and clarified in the documentation that, by default, translate()
assumes that the first codon in a DNA or RNA sequence is the initiation codon. I guess it's too late to switch the default back to the old behavior.
The no.init.codon
option is in Biostrings 2.50.1 (BioC 3.8, current release) and Biostrings 2.51.1 (BioC 3.9, current devel).
H.
Thanks for the fix ! Should I close that issue myself ?
Closing it now.
Hello,
Since at least Biostring 2.42, the function "translate" gives wrong results for triplets TTG and CTG.
=> Both should be L (leucine).
We think it's related to the erroneous default use of alternative genetic codes.
Cheers,
Seb