Scientific Tools

Calculate primer melting temperature using nearest-neighbor thermodynamics. QC checks for GC content, self-complementarity, hairpins, and primer dimers. Export one-page assay cards.

Compute relative gene expression using the ΔΔCt (2^-ΔΔCt) method. Import RDML files or paste Ct values. Efficiency correction, outlier detection, and MIQE reporting checklist.

Plan restriction enzyme digests with 250+ enzymes from REBASE. Methylation sensitivity warnings, star activity assessment, buffer compatibility for double digests, gel simulation, and annotated linear/circular sequence maps. IUPAC degenerate base support.

Generate publication-quality annotated DNA sequence maps. Circular and linear views with restriction sites from 250+ enzymes, ORF detection across all six reading frames, custom features (GenBank-style), and primer binding site mapping. SVG and CSV export.

View Sanger sequencing chromatograms from .ab1 files. See per-base quality scores, trim low-quality ends, export to FASTA.

Open and validate RDML files from any qPCR instrument. View amplification curves, extract Cq values, and export to CSV. Supports RDML 1.1–1.4.

Estimate the fraction of error-free PCR product after N cycles for any polymerase. Branching-process model with vendor-published per-base error rates for Q5, KAPA HiFi, Phusion, Platinum SuperFi II, Pfu, OneTaq, and Taq. Side-by-side comparison and CSV exports.

Reverse-solve reads-per-sample, samples-per-run, runs-needed, and cost-per-sample for any NGS project. Compare Illumina NovaSeq X / NextSeq 2000 / MiSeq, Element AVITI, ONT PromethION, and PacBio Revio side by side. Lander–Waterman C = L·N / G with manufacturer-published throughputs.

Free nucleic acid calculator: mass ↔ moles ↔ copies, OD₂₆₀ → concentration, ligation insert mass, C₁V₁ = C₂V₂ dilution, and copies ↔ ng for qPCR standards. Toggle dsDNA / ssDNA / ssRNA / dsRNA. Five tabbed modes, CSV export.

Calculate the optimal incubation temperature for thermostable ligase reactions (OLA, LDR, padlock probes). Nearest-neighbour Tm with salt correction for upstream and downstream probes, mismatch discrimination warning. Supports Taq DNA Ligase, 9°N DNA Ligase, and Ampligase. CSV export.

Calculate optimal fragment volumes for Gibson Assembly and HiFi DNA Assembly reactions. Equimolar or max-input modes, per-fragment volume tables with molar calculations, incubation guidance, printable protocol, and CSV export. Supports 2–15 fragment assemblies.

Validate LAMP primer sets before ordering: nearest-neighbour Tm (SantaLucia 1998), GC content, length constraints, 3′-end stability, and pair Tm differences per Notomi guidelines. Pass/fail flags for F3, B3, FIP, BIP, LF, and LB primers. CSV export and shareable URLs.

Design primers for Gibson Assembly and HiFi DNA Assembly cloning. Nearest-neighbour Tm optimization for binding regions, automatic overlap extensions from adjacent fragment sequences, self-dimer checks, and IDT-compatible CSV export.

Design Golden Gate (Type IIS) assemblies with optimized 4-bp fusion site overhangs scored by the Potapov 2018 ligation fidelity matrix. Generates primers with BsaI, BsmBI, SapI, or BbsI extensions. CSV and FASTA export.

Design mutagenic primers for site-directed mutagenesis. Supports Q5 (back-to-back) and QuikChange (overlapping) methods. Point substitution, insertion, deletion, and block substitution. Mismatch-aware annealing Tm, hairpin and GC warnings, CSV export.

Design complete LAMP primer sets (F3, B3, FIP, BIP, LF, LB) from a target DNA sequence. Sliding-window algorithm with Tm/GC optimization, Notomi distance constraints, top-N ranked alternatives. CSV export.

Design DNA oligos for in-vitro transcription of CRISPR sgRNAs. Supports SpCas9, SpCas9-NG, and SaCas9. Generates forward/reverse oligos with T7 promoter, annealing protocol, and IDT-compatible order sheet.

Check NGS index/barcode compatibility for multiplexed sequencing. Evaluate per-cycle color balance, Hamming distance matrix, and minimum diversity for 4-channel, 2-channel, and 1-channel Illumina chemistries.

Design tiled antisense probes for rRNA or custom RNA depletion. Set probe length, tiling overlap, and clustering threshold. Exports probe FASTA, IDT order CSV, and design parameters. All computation is client-side.

Browsable reference library of commonly used plasmid vectors and DNA molecules. Annotated circular SVG maps, feature tables, FASTA and GenBank downloads. Filter by category, host organism, or selection marker. All data is client-side.

Searchable database of over 250 restriction enzymes. Filter by name, recognition sequence, overhang type, enzyme classification, cut frequency, methylation sensitivity, and isoschizomer relationships. Sortable results with CSV export. All data is client-side.

Predict DNA oligo melting temperature using three nearest-neighbor parameter tables (SantaLucia 1998, Sugimoto 1996, Breslauer 1986). Reports consensus Tm ± spread. Supports batch upload of up to 5,000 sequences.

Build a PLS calibration from Raman spectra and known mRNA concentrations, then predict unknowns with 95% prediction intervals and Hotelling T² / Q-residual outlier diagnostics. Accepts SPC, JCAMP-DX, and CSV. Runs entirely in the browser.