Codon Calculator
Calculate protein length and basic properties from DNA/mRNA codons. A codon is 3 nucleotides encoding one amino acid. Find number of codons, protein length, and expected molecular weight from sequence length.
🧬 Molecular Biology📐 protein length = (ORF length - 3) / 3🧬 Biology
ORF length (bp including stop codon)
Or mRNA/CDS length (nt)
Number of codons (optional — leave ORF blank)
Please enter valid values.
Formula & Reference
| Variable | Symbol | Formula | Units |
|---|---|---|---|
| Codon Calculator | — | protein length = (ORF length - 3) / 3 | amino acids |
Step-by-Step Examples
Example 1
Standard ORF
ORF of 750 bp (including stop codon).
- Codons = 750/3 = 250 codons total
- Protein = 250 - 1 (stop) = 249 amino acids
- MW ≈ 249 x 110 = 27,390 Da ≈ 27.4 kDa
✓ 249 aa protein, ~27.4 kDa
Example 2
Large Protein
ORF = 3600 bp.
- Codons = 3600/3 = 1200 total
- Protein = 1199 amino acids
- MW ≈ 1199 x 110 = 131,890 Da ≈ 132 kDa
✓ 1199 aa protein, ~132 kDa
Example 3
Minimum Viable ORF
Smallest meaningful ORF: Start (ATG) + coding + Stop = 9 bp (encodes 2 aa).
- 3 codons total: Met + 1 AA + Stop
- Encodes 2 amino acids (dipeptide)
- Too short to fold — need at least 50-100 aa for stable protein
✓ Minimum ORF = 9 bp, 2 aa dipeptide
Real-World Applications
Molecular Cloning
ORF size determines vector requirements and protein expression system choice.
Bioinformatics
ORF finding tools scan sequence for potential start codons and reading frames.
Proteomics
Peptide count from in silico tryptic digestion depends on protein length.
Clinical Genomics
Frameshift mutations alter ORF length and produce truncated or aberrant proteins.
Common Mistakes to Avoid
⚠️
Off-by-one error with stop codon
The stop codon is a codon but does NOT encode an amino acid. Protein length = total codons - 1.
⚠️
Confusing codons with bases
1 codon = 3 nucleotides. A 100-codon ORF is 300 bp. This is a very common source of 3x errors.
⚠️
Forgetting the start Met is already counted
The first codon (ATG) encodes Met. Protein length already includes it. No need to add or subtract Met separately.
Frequently Asked Questions
What are the 64 codons? ▾
61 sense codons encode the 20 amino acids (some amino acids have multiple synonymous codons), plus 3 stop codons: UAA (ochre), UAG (amber), UGA (opal).
What is codon bias? ▾
Different organisms prefer different synonymous codons. E. coli prefers CGU for Arg; humans prefer CGG. Matching host codon usage optimizes protein expression.
What is the genetic code degeneracy? ▾
Most amino acids are encoded by 2-6 codons (e.g., Ser has 6: UCU, UCC, UCA, UCG, AGU, AGC). Only Met and Trp have a single codon each.
What is a reading frame? ▾
A reading frame is one of three ways to read a DNA sequence in groups of 3. ATG CGA TTA CGA vs A TGC GAT TAC GA vs AT GCG ATT ACG. Only one frame gives the correct protein.
What is a frameshift mutation? ▾
Insertion or deletion of bases not in multiples of 3. Shifts the reading frame, changing all downstream codons. Usually produces a truncated or non-functional protein.