Analyze DNA sequences with GC content, open reading frame finder, restriction enzyme sites, and protein translation. Compute complement and reverse complement, codon usage tables, and molecular weight — a complete molecular biology workbench built and deployed by an AI agent.
Build Prompt
Copy this prompt into Claude Code
Build a static HTML DNA sequence analyzer. Dark theme: background #0a0a0f, surfaces #12121a, borders #1a1a2a, accent #0891b2.
Main input: large textarea accepting raw DNA sequence (A, T, G, C — strip whitespace, uppercase, reject invalid chars with error message).
Analysis panels (render all on submit):
1. Basic Statistics: sequence length (bp), nucleotide counts and percentages (A/T/G/C), GC content %, AT/GC ratio, molecular weight (use average nucleotide weight: 330 Da/bp), melting temperature (Tm = 2°C × (A+T) + 4°C × (G+C) for sequences ≤13 bp; Tm = 64.9 + 41 × (G+C−16.4)/N for longer).
2. Complement Sequences: show the 5'→3' complement and reverse complement as colored monospace text with A=green, T=red, G=blue, C=yellow.
3. ORF Finder: scan all 6 reading frames (+1, +2, +3, -1, -2, -3) for start codons (ATG) and stop codons (TAA, TAG, TGA). List all ORFs longer than 30 nt with frame, start position, stop position, length. Highlight the longest ORF. For the longest ORF, translate to protein sequence using the standard genetic code table (hardcode the 64-codon lookup table in JS).
4. Restriction Enzyme Sites: check the sequence for cut sites of 20 common enzymes (EcoRI: GAATTC, BamHI: GGATCC, HindIII: AAGCTT, NotI: GCGGCCGC, XhoI: CTCGAG, NcoI: CCATGG, XbaI: TCTAGA, SalI: GTCGAC, PstI: CTGCAG, KpnI: GGTACC, SacI: GAGCTC, ClaI: ATCGAT, SpeI: ACTAGT, ApaI: GGGCCC, MluI: ACGCGT, NheI: GCTAGC, AgeI: ACCGGT, BglII: AGATCT, EcoRV: GATATC, SmaI: CCCGGG). List enzyme, recognition sequence, cut count, and all positions.
5. GC Content Window Plot: an SVG bar chart showing GC% in sliding 10-bp windows across the sequence length.
Include sample sequence buttons (E. coli lacZ fragment, BRCA1 exon snippet, GFP coding sequence) with hardcoded 60-bp examples.
SEO: title "DNA Sequence Analyzer — GC Content, ORF Finder, Restriction Sites", JSON-LD SoftwareApplication schema.
Read the guide at https://accessagent.ai/api/guide and follow it to deploy the site to AccessAgent.ai. My email is [your@email.com].
Make It Yours
FASTA File Upload
Accept FASTA format file uploads so researchers can analyze sequences from exported databases.
Primer Design Tool
Suggest PCR primer pairs around a target region with Tm matching and GC clamp analysis.
Secondary Structure Prediction
Predict RNA secondary structure hairpins and stem-loops from the transcribed mRNA sequence.
Codon Optimization
Suggest codon-optimized variants of coding sequences for expression in E. coli or human cells.
Pairwise Alignment
Align two input sequences with Needleman-Wunsch and display identity, gaps, and mismatches.
Blast-Link Button
Add a "Search BLAST" button that opens NCBI BLAST in a new tab with the sequence pre-filled.
Update Prompt
Update Prompt — Add protein translation and codon table
Add a full codon usage table panel showing frequency of each codon in the input sequence, grouped by amino acid. Color rare codons (frequency < 10%) in amber. Add a protein molecular weight calculator that takes the translated protein sequence and sums residue masses. Redeploy.
SEO Tips
Target "DNA sequence analyzer online", "GC content calculator", and "restriction enzyme finder" — popular bioinformatics queries.
Write a short explainer on each analysis type (what GC content means, how ORFs are found) for educational SEO.
JSON-LD SoftwareApplication with applicationCategory "Science" and keywords for molecular biology tools.
Submit the tool to bioinformatics tool directories and post in r/bioinformatics and Biostars for backlinks.
Create sample analyses for well-known genes (GFP, CRISPR Cas9) to attract researchers searching those terms.
Monetization Ideas
Affiliate links to reagent suppliers when restriction enzymes are detected (NEB, Thermo Fisher).
Sell a molecular biology reference card PDF with genetic code, IUPAC codes, and common enzyme tables.
Offer batch analysis of multiple sequences as a premium feature for high-throughput researchers.