See Biosmith in action

Animated walkthroughs of 12 key workflows — from Gibson assembly and CRISPR design to AI auto-annotation and the built-in AI assistant.

app.biosmith.app/gibson
Gibson Assembler
Fragment A
ATGAAAGCAATTTTCGTACTGGCTTACTG
Fragment B
GCTTACTGATCAGTACGAATGCCTAG
Fragment C
GAAGATCGAATGCAATCGGTAGCATC
Primer Pairs
Fragment A Tm: 62.3°C
Fwd: ATGAAAGCAATTTTCGTACTG
Rev: GCTTACTGCATCGGTATGCA
Fragment B Tm: 60.8°C
Fwd: GCTTACTGATCAGTACGAATGC
Rev: GAAGATCGTTAGCGATCCAT
Fragment C Tm: 61.5°C
Fwd: GAAGATCGAATGCAATCGGTAG
Rev: CATCGGTAGCATCGATCTAA
Export IDT CSV
Assembly Diagram
Fragment A
Fragment B
Fragment C
◀▶ 25 bp overlap 25 bp overlap ◀▶

Gibson Assembly workflow

  1. 1Enter fragment sequences in the three input fields
  2. 2Sequences type in with 25 bp overlap regions highlighted in teal
  3. 3Click "Design Primers" to calculate primer pairs with SantaLucia Tm values
  4. 4Primer cards appear with overlap regions clearly marked
  5. 5Export directly to IDT — ready-to-order CSV, no reformatting
  6. 6Assembly diagram shows fragment order and overlap junctions

Try Gibson Assembly free — no account needed.

Open Gibson Assembler →
app.biosmith.app/crispr
CRISPR Analyser — SpCas9 / NGG PAM
Target DNA sequence (60 bp)
ATGCGATCGATCGATCGAATCGATCGATCGTAGCGATCGATCGATCGAATCGTAGCGAT
Scoring guides...
Guide RNA candidates
Guide (20 nt)PAMOn-targetOff-target
ATCGATCGATCGATCGAATC TGG 0.72 2 ⚠
CGATCGAATCGATCGATCGT AGG 0.85 0 ✓
GCGATCGATCGATCGAATCG CGG 0.61 4 ⚠
TAGCGATCGATCGATCGAAT TGG 0.79 1 ✓
★ Best guide: row 2 (score 0.85, 0 off-target sites)

CRISPR guide RNA design

  1. 1Paste your 60 bp target DNA sequence into the analyser
  2. 2Click "Analyse" — Biosmith scans all NGG PAM sites and scores each candidate guide
  3. 3Guide RNA table loads with on-target efficiency scores and off-target counts
  4. 4PAM sites highlighted in amber, pass/warn badges for quick triage
  5. 5Best guide (score 0.85, zero off-targets) auto-highlighted in teal

Works for SpCas9, SaCas9, and Cpf1 PAM sites.

Open CRISPR Analyser →
app.biosmith.app/restriction-map
pUC19 — 2686 bp
EcoRI 1204 BamHI 417 HindIII 447 NcoI 2533 pUC19 2686 bp MCS AmpR ori
EcoRI — selected
Enzyme Overhang Position
EcoRI 5'…AATT…3' 1204
Predicted gel fragments
Ladder
Sample
~250 bp ~430 bp ~750 bp ~1256 bp

Restriction map workflow

  1. 1Circular plasmid map loads with MCS, AmpR, and ori regions marked
  2. 2Enzyme sites pop onto the map: EcoRI, BamHI, HindIII, NcoI — each with position
  3. 3Click EcoRI — an animated cursor selects the site
  4. 4Enzyme detail panel shows cut site, 5' AATT overhang, and position 1204
  5. 5Virtual gel bands animate in showing predicted fragment sizes

Supports 200+ restriction enzymes. Single-cutter filter included.

Open Restriction Map →
app.biosmith.app/codon-optimiser
Codon Optimiser
Protein sequence
MKALSVQIRLQPFEEGKVHALTDSP
Target organism
Human (Homo sapiens)
E. coli K12
Human (Homo sapiens)
Mus musculus
CHO cells
Optimised DNA sequence
ATGAAGGCCCTCTCAGTCCAGATCCGGCTGCAGCCATTCGAGGAGGGCAAGGTGCACGCCCTCACCGACTCCCCC
Codon Adaptation Index (CAI) 0.87
52%
GC Content
75 bp
CDS Length
High
Diversity
Copy sequence Export FASTA

Codon optimisation workflow

  1. 1Enter your protein sequence (single-letter amino acids)
  2. 2Choose target organism — 42 options including Human, E. coli, CHO, and yeast
  3. 3Click "Optimise" — Biosmith selects the highest-usage codon at each position
  4. 4Optimised DNA sequence appears, CAI metre animates to 0.87
  5. 5GC%, CDS length, and codon diversity scores shown at a glance
  6. 6Copy to clipboard or export as FASTA — ready for synthesis

CAI scoring against 42 organisms. Optimises for expression, not just frequency.

Open Codon Optimiser →
app.biosmith.app/golden-gate
Golden Gate Designer BsaI ✓
Fragment 1
Promoter
Fragment 2
5'UTR
Fragment 3
CDS
Fragment 4
Terminator
Fusion overhangs
GGAG GCTT AATG TTCG
PCR primers
Promoter
F: GGAGATCGATCGATCG
R: CATCGATCGATCGAAGC
5'UTR
F: GCTTGTACGATCGATCG
R: CATCGATCGAATGCAT
CDS
F: AATGGCGATCGATCGAT
R: CGATCGATCGTTCGAT
Terminator
F: TTCGATCGATCGATCGA
R: CGATCGATCGATCGAA
Compatibility matrix
1
2
3
4
1
✓
✓
✓
✓
2
✓
✓
✓
✓
3
✓
✓
✓
✓
4
✓
✓
✓
✓
Export IDT CSV

Golden Gate Assembly workflow

  1. 1Name your 4 fragments — Promoter, 5′UTR, CDS, Terminator
  2. 2BsaI selected as the Type IIS enzyme; click "Design"
  3. 3Four unique 4-base fusion overhangs appear: GGAG, GCTT, AATG, TTCG
  4. 4PCR primer cards for each fragment show the overhang appended to the annealing sequence
  5. 5Compatibility matrix confirms all 4 overhangs are orthogonal — no mis-ligation
  6. 6Export IDT CSV for one-click ordering

Supports BsaI, BbsI, BsmBI, and Esp3I. Checks overhang orthogonality automatically.

Open Golden Gate Designer →
app.biosmith.app/batch-primers
Batch Primer Designer
Sequencing Check PCR qPCR
Target regions
CMV promoter
GFP
WPRE
AmpR
pMB1 ori
Designing...
Primer results
RegionForwardReverseTm
CMV prom. ATCGATCGATCGATCG CGATCGATCGATCGAT 60.2°C
GFP GATCGATCGATCGATC ATCGATCGATCGATCG 63.1°C
WPRE TCGATCGATCGATCGA GATCGATCGATCGATC 58.9°C
AmpR CGATCGATCGATCGAT TCGATCGATCGATCGA 61.4°C
pMB1 ori ATCGATCGATCGATCG CGATCGATCGATCGAT 59.7°C
Export IDT CSV (10 primers)

Batch primer design workflow

  1. 1Select mode — Sequencing, Check PCR, or qPCR
  2. 2Type 5 target region names: CMV promoter, GFP, WPRE, AmpR, pMB1 ori
  3. 3Click "Design All" — all 5 pairs designed simultaneously
  4. 4Forward and reverse sequences populate with SantaLucia Tm values
  5. 510 primers exported as a single IDT CSV — ready to order in one click

Design up to 96 primer pairs in one batch. Tm-matched pairs guaranteed within ±2°C.

Open Batch Primer Designer →
app.biosmith.app/protein-analysis
Protein Analysis
Amino acid sequence
MKALSVQIRLQPFEEGKVHLSAVREQ
Kyte-Doolittle hydrophobicity
1 26 +4 0
Hydrophobic Hydrophilic
Chou-Fasman secondary structure
α-helix
β-sheet
coil
■ Helix 38% ■ Sheet 27% ■ Coil 35%
3.2 kDa
MW
7.4
pI
28.3
Instability (stable)

Protein analysis workflow

  1. 1Paste a single-letter amino acid sequence (26 residues shown)
  2. 2Kyte-Doolittle hydrophobicity plot draws itself left to right
  3. 3Hydrophobic regions shade amber, hydrophilic regions shade blue
  4. 4Chou-Fasman bar shows predicted secondary structure — helix, sheet, coil
  5. 5Property cards fade in: MW 3.2 kDa, pI 7.4, instability index 28.3 (stable)

Full Expasy ProtParam equivalence — MW, pI, extinction coefficient, GRAVY score.

Open Protein Analysis →
app.biosmith.app/sdm
SDM Designer
Original sequence
ATGAAAGCAATTTTCGTACTGGCTCAGCCA
Mutation (codon position)
A142G
Mutagenic forward primer
ATGAAAGCAATTTTCGTGCTCAGCCATTTCGACTG
A→G substitution at position 142 mutated base
Primer quality 88%
63.2°C
Tm
52%
GC%
28 bp
Length
Add to IDT cart
Order summary
Mutagenic primer (28-mer)× 1 Scale: 25 nmol, standard desalting$8.50

Site-directed mutagenesis workflow

  1. 1Paste the original DNA sequence into the SDM designer
  2. 2Enter the mutation in standard notation — A142G
  3. 3Mutagenic primer appears with the substituted base highlighted in red
  4. 4Primer quality bar animates to 88% — Tm 63.2°C, GC% 52%, length 28 bp
  5. 5Add to IDT cart with one click — order summary confirms scale and price

Supports substitution, insertion, and deletion mutations. QuikChange-compatible design.

Open SDM Designer →
app.biosmith.app/gel-simulator
Gel Simulator
Ladder
Digest A
Digest B
10k8k6k4k 3k2k1.5k1k 750500
2800 bp
Digest A — 4200, 2800, 950 bp Digest B — 5100, 2850 bp

Virtual gel simulation workflow

  1. 1Ladder bands appear first — 10 standard markers from 500 bp to 10 kb
  2. 2Digest A bands grow in: 3 fragments at 4200, 2800, and 950 bp
  3. 3Digest B bands appear: 2 fragments at 5100 and 2850 bp
  4. 4Hovering the 2800 bp band pulses it and shows a size tooltip
  5. 5Compare lane patterns instantly against the ladder — no wet gel needed

Add any digest, import band sizes from Biosmith restriction maps, export as PNG.

Open Gel Simulator →
app.biosmith.app/blast
BLAST Search Blastn ▾
Query sequence (40 bp)
ATGAAAGCAATTTTCGTACTGGCTCAGCCATTTCGAGATC
Searching... RID: ABC123 NCBI nr
Top hits
Organism / accessionIdentityE-value
E. coli K-12 U00096 99% 0.0 ★
pUC19 L09137 98% 2e-18
pBR322 J01749 87% 4e-9
pACYC184 X06403 82% 1e-6
Import to Biosmith

BLAST search workflow

  1. 1Paste a 40 bp query sequence into the BLAST panel
  2. 2Select Blastn and click "Search NCBI" — a progress bar tracks the RID request
  3. 3Results appear row by row: organism, accession, identity %, and E-value
  4. 4Top hit (E. coli K-12, 99% identity) highlights in teal automatically
  5. 5Click "Import to Biosmith" — the hit sequence loads directly into the sequence editor

Blastn, Blastp, Blastx, and tBlastn all supported. Results import directly into your project.

Open BLAST Search →
app.biosmith.app/annotate
AI Auto-Annotator 152 known vector elements
pLenti-CMV-GFP (4,756 bp)
CMV GFP WPRE AmpR ori
Scanning 4,756 bp… 100%
CMV promoter promoter 99.4% Add ✓
GFP CDS 99.4% Add ✓
WPRE misc_RNA 99.4% Add ✓
AmpR CDS 99.4% Add ✓
pMB1 ori rep_origin 99.4% Add ✓
Add All 5 Features ✓ Added to plasmid

AI Auto-Annotator

  1. 1Load plasmid — bare backbone with no annotations displayed
  2. 2Click "Scan Plasmid" — AI screens 4,756 bp against 152 known elements
  3. 3Review matches — 5 features appear as colour-coded cards and arcs on the map
  4. 4Click "Add All 5 Features" — annotations committed to the plasmid in one step

152 curated vector elements including promoters, resistance genes, reporters, and origins of replication.

Try Auto-Annotator →
app.biosmith.app/assistant
AI Assistant Context: pLenti-CMV-GFP (4,756 bp, 5 features)
What promoter drives GFP expression in this construct?
GFP expression is driven by the CMV (cytomegalovirus) immediate-early promoter at positions 14–590. This is one of the strongest constitutive promoters for mammalian cells — you'd expect robust expression in HEK293T, CHO, and most primary human cells. The WPRE element downstream of GFP (positions 1,847–2,435) further boosts expression ~3–5× by enhancing mRNA stability.
Design sequencing primers for GFP
Sequencing primers for GFP (positions 720–1,447):
Primer Sequence Tm
GFP-Fwd ATGGTGAGCAAGGGCGAGGA 64.1°C
GFP-Rev TTACTTGTACAGCTCGTCCA 62.8°C
Copy primers Add to Primer Collection

AI Plasmid Assistant

  1. 1Ask a question — the assistant has full context of the loaded plasmid and its annotated features
  2. 2AI analyses context — reads feature positions, orientations, and known element properties
  3. 3Get an answer with primers, positions, or design suggestions — copy or save directly to your project

Ask about expression levels, cloning strategies, sequencing primers, or troubleshooting. The assistant reads your actual construct.

Try AI Assistant →