Calculate CAI with complete codon provenance
Set up complete CDS sources, choose fixed CAI parameters and retain every gene status with its original codon positions.
Declare the complete sources
Supply complete UTF-8 gene and reference FASTA, or choose the original 61 E. coli weights or an explicit codon,weight CSV. Each active role uses one complete paste or one local file. Preserve case, CRLF, BOM, full headers, IDs and byte identity; IDs are unique within each role.
| Mode | Active sources, in order | Weights and STOP boundary |
|---|---|---|
| reference | genes + references | Complete reference counts build all 64 entries; raw 0 and smoothed 0.5 stay separate; indexed STOP participates. |
| legacy61 | genes | Table 1 only; use the original 61 weights. Missing TAA/TAG/TGA remain null and are skipped by the literal rule. |
| explicit | genes + weights | Use only supplied positive finite weights; retain original decimal lexemes/spans and do not fabricate missing entries. |
Choose frames and the upstream policy
All six parameters are explicitly captured: mode, one of 27 DNA tables, gene and reference forward frames 0/1/2, upstream-indexed STOP policy and report language. No species reference is inferred, tails trimmed or ambiguous bases accepted. Empty CDS, tails, duplicate IDs, invalid UTF-8 or invalid weights fail the complete task.
Keep undefined records and all weights
Keep raw zero counts separate from smoothed 0.5. Preserve original protein-group order, with STOP last overwriting dual-coding weights. Literal ATG/TGG are excluded under every table. Three missing STOP weights in the original legacy index remain null. A zero-eligible gene keeps null CAI/log CAI, denominator 0 and all positions.
Inspect and retain the complete result
Every gene, reference and codon is addressable by record and page. Original sources and all 64 weights are complete.
Complete delivery includes cai-report.json, cai-codons.csv, cai-genes.csv, cai-weights.csv, genes-source.fasta, active references-source.fasta or weights-source.csv (no second source for legacy mode), settings.json and full dual licenses in NOTICE.txt. Copy is the entire JSON. Packed columns are canonical base64 uint8/uint32LE, with no sampled rows.
CSV retains exact IDs and RFC4180 quoting. Import identifier columns as text in spreadsheet applications. JSON and source downloads retain complete original content.
| File | Complete content | Read alongside |
|---|---|---|
| cai-report.json | All source identities, params, table, groups, 64 weights, records and canonical packed columns | Copy contains this complete JSON. |
| cai-codons.csv | Every gene/reference codon, three original byte/line/column positions, counts, weights and denominators | Join by source, record and codon ordinals. |
| cai-genes.csv | Every original ID, CAI/log CAI/log sum, actual denominator and status | Keep null rows with denominator 0. |
| cai-weights.csv | All ACGT64-order weights, raw/smoothed counts, groups and supplied literal spans | Missing entries remain null, never an invented 1. |
| genes-source.fasta + references-source.fasta / weights-source.csv | Complete original active-source bytes; legacy61 has no second source | Download names are fixed; report keeps original name, MIME, lastModified and SHA. |
| settings.json + NOTICE.txt | All effective params, profile, table, core pins, source identities and full dual licenses | Retain with the original sources and complete report. |
Joint gates and recovery
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.
Run reads complete local bytes. Capture, reads, hashing, loading, calculation, full exports, validation, cleanup and first display share one 180-second period.
Correct the full input or choices and run again. Each run creates a fresh worker; selected Files can be reused.
Ten million bases and four million complete triplets cannot be reached together because each codon needs three bases; both original gates remain. Numeric work units are not total CPU instructions. Metadata reservations are estimates; real capacity, native peaks and the complete browser matrix require independent acceptance.
- Check sourceOrdinal and recordOrdinal before reading full headers, frame prefixes and original positions.
- Correct the complete input after tails, ambiguity, duplicate IDs, missing required sources or invalid weights; do not use partial output.
- After cancellation or timeout, rerun the complete source with all six explicit parameters; the original File can be reused.
- Keep every download. Joint gates and reservations do not establish real capacity or Native lifecycle acceptance.
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.