Complete codon adaptation index
Calculate CAI from complete DNA CDS and declared references or weights; retain every gene status, all 64 weights, original bytes and codon positions.
Before you start
Calculate CAI from complete DNA CDS and declared references or weights; retain every gene status, all 64 weights, original bytes and codon positions.
How to use this tool
- Declare mode, genetic code and forward frames; provide complete active sources.
- Run, then inspect every gene status, all 64 weights and original positions.
- Copy complete JSON and download every source, settings, CSV and notice.
Supported inputs and limits
Joint gates: 64 MiB input; 10,000 genes and 10,000 references; 10 million bases; 4 million codons; 64 supplied weights; 40 million numeric work units. Representation and memory gates also apply.
All physical files total 256 MiB; complete text and copy each 256 MiB; complete escaped typed JSON 512 MiB; aggregate 1,280 MiB; wire 4 GiB; owned 1,536 MiB; one 180-second period. These gates do not prove simultaneous maximum capacity.
Each active role uses one complete paste or one local file. Unambiguous ACGT, IDs unique within each role; no tail trimming, species inference or fabricated STOP weights.
Literal Biopython 1.85 CAI leaves; all 27 DNA tables and original Biopython 1.81 legacy weights. Full dual licenses are in NOTICE.txt.
Worked example
Example input
>gene1 ATGGCCGCTTAA >gene2 ATGTGG
Example options
reference / table 1 / frame 0
Example output
gene2: undefined, denominator 0; all original positions retained.
When something does not work
Correct the full input or choices and run again. Each run creates a fresh worker; selected Files can be reused.
Frequently asked questions
Are all STOP codons excluded?
Indexed STOP codons participate. Only absent literal TAA/TAG/TGA are skipped. Literal ATG/TGG are excluded under every table.
What happens to a gene with no eligible codons?
Keep the complete record and positions with null CAI/log CAI, denominator 0 and a warning. Other fatal failures produce no successful partial exports.