A Sequence Workbench for Cloning, CRISPR & Primer Design

Generate composition, ORF, restriction-site and primer summaries from one sequence.

Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning.

Apply one operation to every record in a multi-FASTA and export a single CSV/TSV table.

Chain several tools into a pipeline and run it over every record in a multi-FASTA.

Scan a coding sequence for premature stops, cryptic RBS/polyA signals, unwanted restriction sites, GC extremes and repeats.

Paste any unknown sequence and get a full identity report, then send it to BLAST.

One untreated control against 24-96 edited wells and one sortable table out: indel, base-editing or knock-in percentage per well, each with the fit numbers behind it.

Digest level-0 part plasmids with a Type IIS enzyme and let the overhangs decide the assembly order.

Turn one variant description into one oligo order table: the primers that build it and the primers that genotype it.

Paste the recipe you ran and the sequence you got. It re-runs the assembly from the parts and diffs the whole molecule against your claim.

Calculate the reverse, complement or reverse complement of a DNA/RNA sequence.

Clean, case-convert, wrap, reverse and convert between DNA and RNA.

Generate random sequences with an optional GC target.

Search a sequence for a motif with IUPAC codes, mismatches and both strands.

Paste a GenBank, RefSeq or UniProt accession and get the FASTA or GenBank record.

Convert between FASTA, GenBank and tab-separated formats, and extract CDS or protein sequences.

Translate a nucleotide sequence to protein in any or all six reading frames.

Score a coding sequence's codon usage against an expression host, before optimising.

Find open reading frames in all six frames and translate them.

Optimise a protein or CDS for expression in E. coli, human, yeast, CHO, Pichia and more.

Back-translate a protein to DNA using most-frequent or degenerate IUPAC codons.

Calculate GC%, AT% and per-base composition for DNA or RNA.

Estimate primer Tm, GC% and molecular weight from a sequence.

Nearest-neighbor Tm, ΔG, hairpins and primer dimers for any oligo or primer pair.

Fold one oligo, or two together, with ViennaRNA's loop model at your annealing temperature — hairpin, self-dimer and heterodimer ΔG, plus the interaction ΔG.

Design ranked PCR primer pairs from a template, with Tm, GC and dimer checks.

Design SDM primers from a nucleotide or amino-acid change, QuikChange or Q5 style.

Find recognition and cut sites for common restriction enzymes.

Pick two restriction enzymes and get the single buffer that runs both, each enzyme's activity in every buffer, and a straight answer on when to digest sequentially instead.

Summarise and validate FASTA or FASTQ: counts, N50, GC, quality.

Convert between mass, moles, molarity and copy number for DNA/RNA.

Turn a 3:1 insert-to-vector molar ratio into the microlitres you actually pipette, for one insert or a whole multi-fragment assembly.

Enter a template and two primers to predict the PCR product, its size and position.

Scan a sequence for SpCas9, SaCas9 or Cas12a guide candidates with PAMs and scoring.

Screen a guide's protospacer against curated lab reference genomes — SpCas9 hits ranked by CFD, not by mismatch count.

Convert gene symbols, Ensembl, Entrez GeneID, RefSeq and UniProt accessions in batch, and find cross-species orthologs.

Design SpCas9 pegRNAs for any substitution, insertion, deletion or small replacement — spacer, PBS sweep, RTT and 3' extension, PE3 nicking guides, plus twinPE dual-pegRNA design for large edits.

Score every PBS/RTT combination for one prime edit with PRIDICT2.0 and rank the pegRNAs — HEK293 and K562 scores, library percentiles, the full pegRNA, and Golden Gate cloning oligos.

Design knockdown reagents against an mRNA — Reynolds/Ui-Tei-scored siRNAs with ready shRNA cassettes, or 5-10-5 ASO gapmers screened for known liabilities.

Design KASP/ARMS SNP-genotyping primers — two allele-specific forward primers with FAM/HEX tails and an engineered ARMS secondary mismatch, plus a common reverse primer.

Diagnose gel problems (no bands, smearing, wrong size, primer-dimer, degradation) with a fully deterministic symptom guide that links to the right SeqBench tools.

Find CBE (C→T) or ABE (A→G) base-editing gRNAs that place your target base in the editor's activity window, with bystander flags and amino-acid consequences.

Fold an RNA to its minimum-free-energy secondary structure — dot-bracket, MFE, base-pair list and an exportable arc diagram, without installing ViennaRNA.

Search a gene and get its exon/CDS structure, a druggability/disease/drug/trial/paper dossier, and a GTEx + Human Protein Atlas expression fingerprint — all in one page.

Test a gene list for enriched GO terms and Reactome pathways with hypergeometric p-values and BH-FDR correction.

Lay out PCR reactions on a 96-well plate and export a runnable Opentrons protocol or Echo picklist.

Predict the translation initiation rate at every start codon, and design a 5' UTR to hit a target expression level, with OSTIR and ViennaRNA.

Find the restriction digest that tells your intended construct apart from the empty vector, a flipped insert or a mis-assembly — with the bands you would actually be able to read.

Score your 4-base Golden Gate / MoClo overhangs against real published T4-ligase ligation counts: the weakest junction, every risky pair, and how your set compares with a published one.

Locate the exact direct repeats that let a construct recombine away the DNA between them, and build the shortened molecule you would actually recover.

Work backwards from the size you measured: which pairs of priming sites on your template could make a product that big, and can their 3' ends actually extend?

Drop in an unedited control trace and your edited pool's trace and get the indel spectrum, the unedited fraction, and the R² that says whether the decomposition means anything.

Choose one primer pair per target so no two cross-dimerise, every amplicon is separable on the gel, and one annealing temperature serves the whole panel.

308 publicly deposited vectors with their full GenBank feature tables, and 617 parts harvested from them.

No colonies, every clone empty vector, or no PCR band: get the causes your design and your control plates actually implicate, and the cheapest experiment that separates the top two.

Load an unedited control trace and your edited pool's trace and get per-position C→T or A→G percentages, their z-scores against your own run's background, and the detection limit those numbers sit on.

Build a knock-in donor with homology arms around a Cas9 cut site, fold in a PAM-blocking mutation, and get primers that genotype the edit.

Put the intended allele itself in the basis: measure what fraction of the pool carries your knock-in, what fraction is still wild type, and what fraction is NHEJ byproduct — from one control trace and one edited trace.

Screen a whole oligo pool for cross-dimers between members, each oligo's own hairpin and self-dimer, duplicates and Tm spread.

Sliding-window hydropathy plot to spot transmembrane and surface regions.

Compute molecular weight, isoelectric point, extinction coefficient and composition.

Digest a protein with trypsin, Lys-C, chymotrypsin and more, and get peptide masses.

Submit a protein for domain architecture, family and GO-term annotation via EBI InterProScan.

Look up a UniProt accession's AlphaFold prediction, view it in 3D with pLDDT confidence coloring, and highlight residue ranges.

Align several DNA or protein sequences and view a colored alignment with a consensus.

Predict restriction fragments and see the simulated agarose gel with a ladder.

Align a query to a reference and list substitutions, insertions and deletions with effects.

Align two sequences with Needleman-Wunsch or Smith-Waterman.

Render a circular or linear map with restriction sites.

Paste a GenBank record and see an annotated circular or linear map with a feature table.

View an .ab1 / .abi Sanger chromatogram, read the base calls and export the trace.

Align a Sanger read to a reference and get a pass / needs-review verification report.

Align many NGS/Nanopore/Sanger reads to a reference with minimap2, call multi-read consensus variants, and build a corrected consensus sequence.

Paste what you got back and the PCR you say made the insert. It re-derives the insert, finds it in either orientation, and gives you the exact mismatch positions.

Auto-detect promoters, tags, origins and resistance markers in a plasmid, then run a deep scan against pLannotate's full feature databases.

Paste an unlabelled plasmid and get its closest classic backbone, whether it looks like a chimera of two, and every stretch that neither a known backbone nor a known feature accounts for.

Plot log2 fold-change vs. significance from a DESeq2/edgeR/limma table, with draggable thresholds.

Cluster and visualize a gene x sample expression matrix with row/column dendrograms.

Convert an HGVS c. variant to genomic (g.) coordinates and predict its protein (p.) effect, via a real, live Ensembl exon map.

Look up a variant by rsID, chrom:pos:ref:alt, or HGVS and get its ClinVar significance, gnomAD allele frequencies, and CADD/SIFT/PolyPhen2/REVEL scores in one card.

Type or paste a sequence and edit it directly — every feature remaps live as you insert, delete, or replace bases, with undo/redo and GenBank import/export.

Per-base quality, GC and length distributions, duplication levels, overrepresented sequences and adapter content, each with a warn/fail verdict.

Drop a plate of Sanger reads against one construct and get one row per clone: which colonies to grow up, and why.

Screen an unknown plasmid against 30 curated common backbones and rank the candidates by identity and coverage.