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Professional bioinformatics tool: GC content, Melting Temp, ORF Finder, Restriction Sites, Translation

0 bp
Load example:
📊 Basic Statistics
Base Composition
0% GC50%100% GC
🧬 Sequence Manipulations
🔬 Translation: All 6 Reading Frames

M = Start   * = Stop   +1/+2/+3 = forward   -1/-2/-3 = reverse complement

🎯 Open Reading Frames (min 30 codons / 90 bp)
✂ Restriction Enzyme Sites
📖 Codon Usage Table

Codon counts from the input sequence (all three forward reading frames combined).

🏭 Primer Design

Auto-suggests forward and reverse primer pairs from the input sequence. Checks Tm, GC%, length, and self-complementarity (hairpin).

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🔍 Pairwise Alignment (Smith-Waterman local)

Paste two DNA sequences to align. Shows identity %, mismatches, gaps, and a visual alignment.

Sequence A
Sequence B
⚙ Codon Optimization

Rewrites a protein-coding sequence using the most frequent codons for the selected organism. Input must start with ATG.

🔁 Repeat Finder

Detects direct repeats, inverted repeats, and tandem repeats in the loaded sequence.

🧬 CpG Island Detection

Finds CpG-rich regions using the Gardiner-Garden & Frommer (1987) criteria: length ≥200 bp, GC% ≥50%, obs/exp CpG ratio ≥0.6.

🎯 Kozak Sequence Scorer

Scores every ATG codon in the sequence against the consensus Kozak context (GCC)GCCRCCATGG. Rates each as Strong, Adequate, or Weak.

💫 RNA Secondary Structure

Predicts stem-loop / hairpin structures in the RNA transcript using a greedy nearest-neighbor ΔG scan. Identifies the top hairpins by free energy.

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🧲 Amino Acid Properties

For each ORF found in the sequence, shows molecular weight, isoelectric point (pI), GRAVY hydrophobicity score, amino acid composition, and charge at pH 7.