Biostrings - translate gives wrong results for triplets TTG and CTG
1
0
Entering edit mode
@janassebastien-16370
Last seen 5.7 years ago

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

biostrings • 1.3k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

It's fine to track this on github only.

ADD REPLY
0
Entering edit mode
@herve-pages-1542
Last seen 11 hours ago
Seattle, WA, United States

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

H.

ADD COMMENT

Login before adding your answer.

Traffic: 723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6