A Sequence Workbench for Cloning, CRISPR & Primer Design

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.

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

Generate random sequences with an optional GC target.

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.

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

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 — all in the browser.

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.

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.

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.

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

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.

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.