Colour alternative start codons [feature request]

[sjackman]

AUA, AUU, AUC are alternative start codons of the vertebrate mitochondrial code.
See https://en.wikipedia.org/wiki/Vertebrate_mitochondrial_code#Alternative_initiation_codons

[jrobinso]

Should this only be done for mitochondria? I'm not sure how that would be detected, other than chr naming convention, but in principle would that be the right thing?

[sjackman]

Although I said yellow, I think a desaturated pale green may be a better colour.

[sjackman]

Should this only be done for mitochondria? I'm not sure how that would be detected, other than chr naming convention, but in principle would that be the right thing?

Base it on the genetic code (translation table) which is set by right clicking on the sequence. These ATN alternative start codons are for vertebrate mitochondrial.

[sjackman]

Funny. When googling this issue just now I stumbled on this related issue Cryptic ACG start codon #582. That one's trickier because there is no specific genetic code for plant mitochondria, which use the standard genetic code. Perhaps the genetic code could specify a set of default alternative start codons (like for vertebrate mitochondria), and the user could specify additional custom alternative start codons, that may be specific to their particular species.

[jrobinso]

@sjackman Came across this again, I'd like to take care of it for vertebrate mito, but can you point me to an example mitochondrial sequence with annotations? Its hard to test otherwise.

[sjackman]

Great! Here's the human mitochondrial genome. https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1
I don't recall off the top of my head whether it uses any alternative start codons.

[jrobinso]

IGV doesn't fully support genbank format, so the coding sections aren't visualized in IGV (no codons of any kind in the annotation track). However, reading this thread again I think you are primarily focused on the 3 frame translation track under the sequence, correct? I was thinking about the annotation track. Of course both should be in sync.

[jrobinso]

@sjackman I see AUU and AUA here, but not AUC. This might confuse some to color AUC for human. Perhaps I should add specific entries for human, bos taurus, etc.
Or is this opening a can of worms?
https://en.wikipedia.org/wiki/Vertebrate_mitochondrial_code#Alternative_initiation_codons

[sjackman]

Bos: AUA
Homo: AUA, AUU
Mus: AUA, AUU, AUC
Coturnix, Gallus: also GUG[8]

https://en.wikipedia.org/wiki/Vertebrate_mitochondrial_code#Alternative_initiation_codons

Each individual vertebrate species could potentially use a different subset of these three alternative start codons. I haven't done the survey myself. I'd be inclined to colour AUA AUC AUU as yellow for all vertebrate species. Since human is super common, you could perhaps add a special case just for that one species (though I probably wouldn't bother).

[jrobinso]

Well I've spent some time looking at this, I didn't write this code originally so it took some review. Currently its coloring based on the amino acid, not the codon, so it colors Methionine green wherever its found. This works for the standard table because ATG/AUG encodes for M, and nothing else does. But it's not going to work correctly for the Mitochondrial table, or probably others, so this needs some rework.

[sjackman]

Thanks for looking into it, Jim.

[jrobinso]

I think this is sorted out, you can pull and try it.

[sjackman]

Thanks, Jim! Your responsiveness to rather fairly random requests is amazing. Enjoy your Thanksgiving weekend.

[helgathorv]

Released in IGV 2.8.0