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Question: Biostrings - translate gives wrong results for triplets TTG and CTG
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gravatar for janas.sebastien
4 months ago by
janas.sebastien0 wrote:

All,

I also posted that message on Github, since I don't know what's the best place to report potential bugs.

Since at least Biostring 2.42, the function "translate" gives wrong results for triplets TTG and CTG.

translate(DNAString("TTG"))
1-letter "AAString" instance
seq: M

translate(DNAString("CTG"))
1-letter "AAString" instance
seq: M

=> Both should be L (leucine).

We think it's related to the erroneous default use of alternative genetic codes.

Cheers,

Seb

ADD COMMENTlink modified 10 days ago by Hervé Pagès ♦♦ 13k • written 4 months ago by janas.sebastien0

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by janas.sebastien0

Moreover, the documentation does not say that the sequence must be a complete sequence (starting at the start codon).

ADD REPLYlink written 4 months ago by janas.sebastien0

It's fine to track this on github only.

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 22k
0
gravatar for Hervé Pagès
10 days ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

This has been discussed and addressed on GitHub: https://github.com/Bioconductor/Biostrings/issues/15

H.

ADD COMMENTlink written 10 days ago by Hervé Pagès ♦♦ 13k
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