Is a codon outlier a horizontally transferred gene?

No. Codon bias and base composition are poor indicators of transfer; high expression and regional composition produce outliers too. Treat an outlier as a gene worth a closer look.

Why are so many genes called?

The G-test grows with gene length, so a long gene is called for a small departure. Rank by MILC or B for how far a gene departs, and read q only for whether it does.

Is anything uploaded?

No. Every calculation runs in the browser on the records in your project.

Analyze

Codon outliers: genes whose codon usage departs from their own genome

Score every coding sequence of a genome against the genome's own codon usage and find the genes whose choice among synonymous codons that average does not explain. Each gene gets Karlin's B and the length-independent MILC against the pooled usage of the genes, and a G-test of its codon choice within each amino acid, with the false discovery rate controlled across the genes. The ribosomal proteins' rank says whether expression is what separates them.

Open Codon outliers: genes whose codon usage departs from their own genome Open the Codon outliers sample

Every coding sequence of Mycoplasma genitalium and of yeast chromosome I, each scored against its own genome’s codon usage to find the genes that choose codons unlike the rest

What it does

01Karlin's B and the length-independent MILC of every gene against the genome's own pooled codon usage
02A G-test of each gene's synonymous codon choice, χ² on the degrees of freedom of the amino acids it uses
03Benjamini–Hochberg or Benjamini–Yekutieli control of the false discovery rate across the genes
04Every NCBI genetic code, and either reading of alternative start codons
05Where the ribosomal proteins rank, as a check on whether expression drives the signal

What it runs on

Checked against coRdon (Bioconductor) and R's p.adjust on every gene of Mycoplasma genitalium and yeast chromosome I. The panel runs on @ports/discover, @ports/workflow.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Is a codon outlier a horizontally transferred gene?: No. Codon bias and base composition are poor indicators of transfer; high expression and regional composition produce outliers too. Treat an outlier as a gene worth a closer look.
Why are so many genes called?: The G-test grows with gene length, so a long gene is called for a small departure. Rank by MILC or B for how far a gene departs, and read q only for whether it does.
Is anything uploaded?: No. Every calculation runs in the browser on the records in your project.

Also searched as

codon usage outliers · codon bias within a genome · MILC codon usage · Karlin B codon bias · genes with atypical codon usage · highly expressed genes codon usage · codon usage G-test · false discovery rate across genes