A Sequence Workbench for Cloning, CRISPR & Primer Design

Apply one operation — or a chain of them — to every record in a multi-FASTA and export a single CSV/TSV table.

Paste a sequence and find out what it is, against the whole of GenBank, with the program chosen for you.

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

Find CpG islands by either published definition, with the observed/expected CpG ratio reported separately from GC content.

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

Read a GFF3 annotation file as a feature table, and turn it plus its FASTA into a GenBank record with an annotated map.

Search for a motif you have, or discover one shared by a set of sequences.

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

Generate random sequences with an optional GC target.

Get the reverse complement, complement and reverse of a DNA/RNA sequence at once.

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

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

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

Translate a nucleotide sequence to protein in all six reading frames at once.

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

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

Render a circular or linear map with restriction sites.

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.

Open a SnapGene .dna file and read its sequence, features, colors and primers — no SnapGene, no account.

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

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

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

Turn an OD600 reading into a cell density, a total cell count, and the volumes for a back-dilution.

Find every sigma-70 promoter in a region on both strands, with the free-energy terms behind each transcription rate — then build a library of promoters spanning a range.

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

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

Find every stretch of a transcript that can pair over the Shine-Dalgarno sequence or the start codon, with the length and melting temperature of each duplex — the mechanism behind every translational switch, and the first thing to check when a construct is silent.

Fold an RNA to its minimum-free-energy secondary structure — dot-bracket, MFE, base-pair list and an exportable arc diagram, with nothing to install.

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

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

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.

Mark the ladder on your gel photograph, click a band, get its size in bp.

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.

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

Which antibiotic, which host, which backbone, and what will bite you later.

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

Find the largest subset of your parts that share no long stretch of sequence, or design new ones that do not — the property that keeps a multi-part assembly stable and synthesisable.

Build a multi-gene operon from a promoter, coding sequences and a terminator, then scan the assembled molecule for the internal promoters, ribosome binding sites and terminators that the joins created.

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

Find recognition and cut sites for common restriction enzymes.

Convert centrifuge speed to relative centrifugal force and back, for any rotor radius.

How many grams to weigh out for a target molarity and volume, with the hydrate trap caught.

Measure the repeats, GC extremes, GC transitions, homopolymer runs and hairpins that make a fragment hard to synthesise — each against the threshold vendors publish, with no score and no probability.

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

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

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.

Inspect chromatograms, compare a read with its reference, or screen a whole plate of clones.

Align your reads to your own annotated reference and get what each difference DOES — silent, missense at a named codon, or a premature STOP that ends the protein — not just where it sits.

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.

Drop the results your sequencing service sent and the map it should be — every sample of the order checked at once.

Design a set of DNA barcodes that are pairwise far enough apart that a read error cannot turn one into another, or check a set you already have for the pair that will collide first.

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

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.

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

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

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

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

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

See repeats, duplications and inversions that a single best alignment hides.

Convert HGVS between c., g. and p.: a c. variant to genomic coordinates and its protein effect, or a genomic position back onto its MANE transcript — via a live Ensembl exon map.

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

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

Build a neighbour-joining tree with bootstrap support, or open a Newick file somebody sent you.

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.

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

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

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

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

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

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.

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

Ct values in, fold change out - with the propagated standard error, and the right method picked for your amplicon efficiencies.

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

Open a .pdb or .cif file — every chain's sequence, missing residues, ligands and pLDDT — or look up a UniProt accession's AlphaFold prediction in 3D.

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

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

Domains, GO terms, transmembrane helices and signal peptide, via EBI InterProScan.

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

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.

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

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.

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

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.

Build a multiplexed CRISPR array that expresses up to 27 sgRNAs from one construct and shares no long stretch with itself — the property that stops it recombining away and getting refused by synthesis vendors.

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.

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

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?

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.

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.

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