As I might have said 27 years ago if there was social media: ANNOUNCING GCUA: General Codon Usage Analysis. I published first version in 1999 & I wrote it in C. The current version is written in python and has a few more bells and whistles, particularly plotly visualizations github.com/mol-evol/gcua - ThreadSky

jomcinerney.bsky.social • 6 days ago

As I might have said 27 years ago if there was social media: ANNOUNCING GCUA: General Codon Usage Analysis. I published first version in 1999 & I wrote it in C. The current version is written in python and has a few more bells and whistles, particularly plotly visualizations https://github.com/mol-evol/gcua

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jomcinerney.bsky.social•6 days ago

it has a "proper" old fashioned interface, but can run on the command line.

jomcinerney.bsky.social•6 days ago

and it can do nice interactive visualizations like this (this is the default correspondence analysis of codon usage, showing the outlier genes whose codon usage is not quite the "canonical" usage pattern).

jomcinerney.bsky.social•6 days ago

These plots pop up in a browser and are a bit interactive (see plotly for all this goodness). This is a plot (of the Plasmodium falciparum protein coding genes) of Effective Number of Codons versus the GC3s content of the gene - sometimes called "Wrights Plot" https://doi.org/10.1016/0378-1119(90)90491-9

jomcinerney.bsky.social•6 days ago

This is a new bit. It is an RSCU Heatmap. Every row is a codon, every column is a gene and the colour is how high or low its RSCU value is. You can see the plot is a bit "banded", this is because alternative -neighboring - codons in this organism are either highly or lowly used

jomcinerney.bsky.social•6 days ago

so, for instance, if you zoom in, you can see the G and C-ending codons tend to be rarely used, while the T and A-ending codons are used more frequent. Just hover over a cell and you can see the underlying data.

jomcinerney.bsky.social•6 days ago

there are other outputs that might be interesting, such as a correlation matrix for the various metrics.

lablabella.bsky.social•6 days ago

Is there a way to implement additional genetic codes?

Codes 12 and 26 are for our weird little yeasties

jomcinerney.bsky.social•5 days ago

it shouldnt be much of a problem. Right now it only has one 'alternative' code, just so i could figure out how i might add in another code. I'll try getting to it as soon as i can.

lablabella.bsky.social•5 days ago

That would be incredibly useful for our group!

It would make it much more accessible for our new trainees

jomcinerney.bsky.social•4 days ago

I have incorporated all the variant codes now. Let me know what you think.

lablabella.bsky.social•4 days ago

Thanks!! I will have my student take a look

cslamo.bsky.social•6 days ago

Will try! Is the input a fasta with CDSs?

jomcinerney.bsky.social•6 days ago

Yes. There is an example dataset (p. falciparum) that you can download from the github site...or use your own data. Let me know how you get on and if you spot any bugs.

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