STOP participation depends on the index
Distinguish the current CAI index, final dual-coding group and original legacy 61 weights.
The original question and the fixed modern method
In archived issue #4337, the author noticed length minus one in a deprecated implementation and planned migration; private genes/references and final outcome are unknown. T366 fixes the modern Biopython 1.85 __init__/calculate methods with original ordinary floating-point order. The historical question does not establish current browser usage or willingness to pay.
Indexed STOP and absent literal STOP
Modern reference mode builds a complete 64-entry index, so indexed STOP participates. Original legacy 61 weights omit TAA/TAG/TGA, which are skipped by the upstream literal rule. Explicit CSV depends on the actual supplied index; globally excluding STOP would change the calculation.
| Condition | Fixed behavior | Inspect in the result |
|---|---|---|
| Literal ATG/TGG | Excluded under all 27 tables, regardless of amino-acid mapping. | excluded-ATG-TGG; no increment to the eligible denominator. |
| Indexed literal TAA/TAG/TGA | Participate using the actual positive weight; no global STOP exclusion. | participates; actual weight and denominator. |
| Absent literal TAA/TAG/TGA | Skipped by the upstream literal rule; absent weight stays null. | absent-literal-STOP; no increment to the denominator. |
| Any other absent codon | The complete task fails; a table STOP flag does not invent a weight or skip rule. | Complete failure details and original positions. |
| Gene with no eligible codons | Keep the complete row with null CAI/log CAI and denominator 0. | undefined-zero-eligible; full source and warning. |
Dual coding and the actual denominator
For dual-coding tables, preserve the original protein-alphabet group order followed by the final STOP overwrite. The report retains final groups, raw and smoothed counts, weights, participation and actual denominators. ATG/TGG exclusions remain literal under every chosen table.
Explain the result with its complete source
Every gene, reference and codon is addressable by record and page. Original sources and all 64 weights are complete.
Correct the full input or choices and run again. Each run creates a fresh worker; selected Files can be reused.
- Compare source mode, table, frames, actual weights and eligible denominator before comparing CAI values.
- Read rawCount separately from smoothedCount (0 versus 0.5); dual coding uses the final STOP-group weight.
- Keep original IDs, full headers, positions, settings and licenses with scores; the historical issue does not disclose private inputs or a final outcome.
References
- Archived original deprecated-denominator question
Complete offline archived source reviewed; private inputs and final outcome unknown.
- Original Biopython 1.85 CAI source
Full original file and selected leaves retained locally.
Tools in this category
Expand a tool to see its steps, options and supported formats, then open its workspace.
Complete codon adaptation indexCalculate CAI from complete DNA CDS and declared references or weights; retain every gene status, all 64 weights, original bytes and codon positions.
Calculate CAI from complete DNA CDS and declared references or weights; retain every gene status, all 64 weights, original bytes and codon positions.
Steps
- 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.
Capabilities 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.