REFERENCE DATA
Codon usage reference.
Nucleora ships 28 empirical codon-usage tables and 5 codon-pair tables in data/codon_tables/. Each usage table is a tally of that organism's RefSeq coding sequences and records how many sequences it was built from. Every figure and every number on this page is computed from those files — see Methods.
The tables
One row per table file. n_CDS is the number of coding sequences that passed the tally filters — it is a sample size, not the organism's gene count. G/C-end is the mean fraction of G- or C-ending codons across the 18 degenerate amino-acid families, an unweighted summary of third-position bias.
| Organism | Genus / species | Catalog category | n_CDS | G/C-end | Table |
|---|---|---|---|---|---|
| Bovine tubercle bacillus | Mycobacterium bovis | Pathogens (antigen source) | 1,229 | 0.774 | |
| Tubercle bacillus | Mycobacterium tuberculosis | Pathogens (antigen source) | 472 | 0.779 | |
| California condor | Gymnogyps californianus | Birds | 250 | 0.452 | |
| Cattle | Bos taurus | Hoofstock / livestock | 250 | 0.537 | |
| Cheetah | Acinonyx jubatus | Big cats | 250 | 0.612 | |
| Bottlenose dolphin | Tursiops truncatus | Other mammals | 250 | 0.677 | |
| Asian elephant | Elephas maximus | Conservation / megafauna | 250 | 0.421 | |
| Gorilla | Gorilla gorilla | Primates | 250 | 0.445 | |
| Green anole | Anolis carolinensis | Reference / lab | 250 | 0.635 | |
| Koala | Phascolarctos cinereus | Other mammals | 250 | 0.538 | |
| Lion | Panthera leo | Big cats | 250 | 0.517 | |
| Pig | Sus scrofa | Hoofstock / livestock | 250 | 0.591 | |
| Red fox | Vulpes vulpes | Wildlife carnivores (oral-bait targets) | 250 | 0.602 | |
| Sheep | Ovis aries | Hoofstock / livestock | 250 | 0.594 | |
| Horse | Equus caballus | Hoofstock / livestock | 249 | 0.530 | |
| Tiger | Panthera tigris | Big cats | 249 | 0.518 | |
| Cat | Felis catus | Carnivores / companion | 248 | 0.591 | |
| Dog | Canis lupus familiaris | Carnivores / companion | 248 | 0.582 | |
| African elephant | Loxodonta africana | Conservation / megafauna | 248 | 0.511 | |
| Ferret | Mustela putorius furo | Carnivores / companion | 248 | 0.411 | |
| Polar bear | Ursus maritimus | Conservation / megafauna | 248 | 0.567 | |
| Rhesus macaque | Macaca mulatta | Primates | 248 | 0.595 | |
| Axolotl | Ambystoma mexicanum | Reptiles & amphibians | 247 | 0.538 | |
| Giant panda | Ailuropoda melanoleuca | Conservation / megafauna | 247 | 0.523 | |
| Chimpanzee | Pan troglodytes | Primates | 241 | 0.530 | |
| White rhinoceros | Ceratotherium simum | Conservation / megafauna | 201 | 0.561 | |
| Giraffe<100 CDS | Giraffa camelopardalis | Conservation / megafauna | 7 | 0.364 | |
| Raccoon<100 CDS | Procyon lotor | Wildlife carnivores (oral-bait targets) | 6 | 0.328 |
No table file carries a build timestamp, so the tally date of all 28 tables is unknown rather than assumed — see Methods › Build dates. Giraffe (Giraffa camelopardalis, 7 CDS) and Raccoon (Procyon lotor, 6 CDS) fall below the 100-CDS floor and are excluded from the comparison figures below; their rows are flagged.
Cross-organism RSCU matrix
Relative synonymous codon usage for every degenerate codon in the 26 tables at or above 100 CDS. RSCU is 1.0 when a codon is used exactly as often as its synonyms, above 1.0 when preferred and below 1.0 when avoided. Columns are grouped into the 18 degenerate amino-acid families. Point at any cell for its organism, codon, RSCU and raw fraction.
What is not in this figure. Met (ATG) and Trp (TGG) are omitted: they have one codon each, so RSCU is 1.0 by definition. The three stop codons are omitted because the tally drops each sequence's terminal codon, so stop frequencies in these files are not terminator usage — 6 of 28 tables have an all-zero stop family. The colour scale is clamped to RSCU 0.25–4.0; the highest attainable RSCU is 6.0, in the six-fold Leu, Arg and Ser families.
Compare one amino acid across organisms
Pick an amino-acid family to see every synonymous codon's usage side by side across the 26 plotted tables. Bars are the within-family fraction; the dashed line marks the unbiased expectation 1/n, where n is the family's degeneracy.
Full table, one organism
All 64 codons for a single organism: the within-family fraction as stored in the file, and the RSCU derived from it. Defaults to Bovine tubercle bacillus, the table with the most coding sequences (1,229 CDS).
Bovine tubercle bacillus
Fractions are stored to four decimal places, normalised within each amino-acid family. Raw codon counts and per-1000 frequencies are not stored in these files and so are not shown — deriving them would require the amino-acid composition, which is not recorded. Why.
Codon-pair (CPS) tables
These 5 files are a different quantity from the usage tables above: they score adjacent codon pairs (dicodons) rather than single codons, after the method of Coleman et al. 2008. n_ref is the number of reference CDSs the scores were learned from; pairs is how many distinct dicodons were observed, out of 3,721 possible pairs of the 61 sense codons.
| File | Organism key | n_ref | Pairs observed | Coverage |
|---|---|---|---|---|
| cps_Homo sapiens.json | Homo sapiens | 0 | 0 | 0.0% |
| cps_chicken.json | chicken | 60 | 3,358 | 90.2% |
| cps_human.json | human | 40 | 2,853 | 76.7% |
| cps_mouse.json | mouse | 60 | 2,952 | 79.3% |
| cps_yeast.json | yeast | 60 | 2,807 | 75.4% |
Defect, reported not hidden. cps_Homo sapiens.json contains n_ref = 0 and zero pairs — a failed build that was written to disk anyway. It carries no usable scores. The working human table is cps_human.json. See Methods › Codon-pair tables.
Check a sequence
The analyzer below runs in your browser. Paste a coding sequence to see composition and design-rule checks fire as you type.
Runs entirely in your browser; nothing is sent anywhere. Input is capped at 2,000 nt.