🧬 Codon Usage Calculator
Analisi codon usage bias e RSCU (Relative Synonymous Codon Usage) da sequenza FASTA o DNA grezzo. Tool client-side: la tua sequenza non lascia il browser.
📝 Sequenza in input
Supporta FASTA (header con >) o DNA grezzo. Solo A/C/G/T (case-insensitive). Altri caratteri ignorati.
📊 Statistiche
Top 10 codoni più frequenti
| Codone | AA | Conteggio | Frequenza % | RSCU |
|---|---|---|---|---|
| GCA | A | 60 | 75.95% | 4 |
| CTG | L | 5 | 6.33% | 5 |
| CAG | Q | 5 | 6.33% | 2 |
| GAG | E | 4 | 5.06% | 2 |
| ATG | M | 2 | 2.53% | 1 |
| TTA | L | 1 | 1.27% | 1 |
| GTA | V | 1 | 1.27% | 2 |
| GTG | V | 1 | 1.27% | 2 |
| TTT | F | 0 | 0% | 0 |
| TTC | F | 0 | 0% | 0 |
RSCU: valore >1 indica preferenza per quel codone tra i sinonimi del suo amminoacido. <1 indica codone sotto-utilizzato. =1 nessun bias.
📚 Per studenti di Bioinformatica
Questo tool fa parte della sezione Università e supporta studenti delle magistrali in Bioinformatica di:
- UniBa - primo corso magistrale Bioinformatica del Sud Italia
- Tor Vergata - Bioinformatica con 1/3 percorso in laboratorio
- Polimi + UniMi - Bioinformatics for Computational Genomics congiunto
Approfondisci la teoria con la serie UniAppunti / Bioinformatica.
Come utilizzare Codon Usage Calculator
Attach a FASTA sequence or rough DNA
Paste a sequence in the text area in FASTA format (with header > or) or simple DNA sequence of bases A, C, G, T. Invalid characters are automatically ignored.
Alternatively load the example sequence
Use the button "Load Example" to populate the field with a pre-made demonstration sequence, useful for immediately understanding the format of the statistics produced.
Read length, GC content and total codons
The tool calculates real-time sequence length, GC content percentage, and total number of translated codons (triplets of bases).
Analyze the top 10 codon table and RSCU values.
Observe the top 10 most frequent codes with their respective amino acid, count, percentage frequency and RSCU value to identify synonymous codon usage bias.
Suggerimenti
- Remove introns and non-coding regions before gluing the sequence, otherwise codon usage statistics will be distorted compared to just the CDS.
- High or low GC content may indicate the origin of the organism: bacteria like some Streptomyces have GC content over 70%, while others remain below 40%.
Domande frequenti
What is codon usage bias and why is it important?
Codon usage bias is the tendency of an organism to preferentially use some synonymous codons (coding for the same amino acid) over others. It is relevant in bioinformatics for optimizing gene expression, designing synthetic constructs, and studying evolutionary sequences.
How is the value of RSCU interpreted?
Relative Synonymous Codon Usage Comparison compares the observed frequency of a codon with the expected frequency if all synonymous codons were used uniformly. A value greater than 1 indicates preference for that codon, a value less than 1 indicates underutilization, and a value of 1 indicates no bias.
Why must the sequence be a multiple of 3?
The codons are triplets of bases: reading occurs in blocks of 3 characters starting from the first position of the cleaned sequence. If the length is not a multiple of 3, the remaining 1 or 2 characters are not counted as complete codon.
Does my genetic sequence leave the browser when I analyze it?
No calculations of GC content, codon count and RSCU are performed on the client-side using JavaScript. The sequence is never sent to any server or saved anywhere.
Does the tool also recognize stop codes?
Yes, stop codons (TAA, TAG, TGA) are included in the standard genetic table used by the calculator and are counted as any other codon in frequency statistics and RSCU.