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Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
Remote server: your requests and data go to seqbench.com. Claude Code: claude mcp add --transport http workbench https://seqbench.com/api/mcp · Claude app: Settings → Connectors → Add custom connector.
The tools this server listed when we connected to it, in its own words.
reverse_complement — Reverse, complement and reverse complement of a DNA or RNA sequence.gc_content — GC content, AT content and per-base composition of a sequence.translate — Translate a nucleotide sequence to protein (single frame or all six frames; standard code).find_orfs — Find open reading frames (ATG…stop) across all six frames.format_sequence — Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.motif_discover — Find a motif NOBODY TYPED: given a set of sequences (multi-record FASTA), report the short pattern they share, as a consensus, a position-wemotif_finder — Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.reverse_translate — Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).random_sequence — Generate a random DNA, RNA or protein sequence, optionally with a target GC content.melting_temperature — Primer/oligo melting temperature: nearest-neighbor (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with thannealing_temperature — Annealing temperature and a full cycling program for a primer PAIR, under the rule the polymerase's own vendor publishes — which is not one oligo_analysis — Full oligo analysis: nearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.in_silico_pcr — Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a primer_design — De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structureqpcr_assay_design — Design a qPCR assay: primer pairs under qPCR's own constraints (70-150 bp product, tightly matched Tm) each with the best hydrolysis (TaqMandna_molarity — Nucleic-acid quantity conversions: molar mass, amount (pmol/nmol), molar and mass concentration, and copy number, from mass ± volume and eitsite_directed_mutagenesis — Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a base substitution, an amino-acid codon swap, or aoligo_pool_screen — Screen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set forcross_dimer — Screen two oligos for the most stable heterodimer (cross-dimer) between them.primer_specificity — Self-hosted e-PCR-style screen for off-target amplicons predicted by a primer pair against the background chosen with `background`: the bundoligo_cofold — Minimum-free-energy structure and ΔG for one oligo (hairpin) or two oligos together (homo/heterodimer), using ViennaRNA's published loop modbarcode_design — Build a set of DNA barcodes that are pairwise at least a chosen edit distance apart, so a read error cannot turn one barcode in the pool intbarcode_audit — Take a set of barcodes and report the minimum edit distance in it, which pairs sit at that distance, any duplicates, the GC range and the lorestriction_sites — Find restriction enzyme recognition sites in a DNA sequence.double_digest — Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.cloning_simulate — Assemble fragments by Gibson/overlap, Golden Gate (Type IIS), restriction–ligation (sticky or blunt), TOPO/TA, LIC or SLIC (T4-polymerase chplasmid_annotate — Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. Signatures under 20 bp musconstruct_qc — Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.construct_autofix — Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeatvirtual_gel — Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.ligation_setup — Work out how many microlitres of vector and insert to pipette to hit a target molar ratio, from each part's length and stock concentration. gel_band_size — Calibrate a gel lane against a marked DNA ladder and read the size of any other band from how far it ran. Migration distance is approximatelexpression_cassette_check — Check the ARRANGEMENT around each coding sequence, which is what decides whether a finished clone expresses at all: a promoter for the namedgolden_gate_from_parts — Golden Gate as the reaction runs: digest pre-domesticated part plasmids with a Type IIS enzyme and assemble them in the order their OVERHANGgolden_gate_library — Every combination of interchangeable part plasmids, assembled. Give the alternatives at each position — three promoters, four coding sequencassembly_outcomes — Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two padiagnostic_digest — Pick the restriction digest that tells your intended construct apart from the wrong ones on a screening gel. Digests every candidate, works repeat_instability — Find the exact direct repeats in a construct that make it deletable, and build the molecule each pair would collapse to. Two copies of the snonrepetitive_parts_find — Given a toolbox of genetic parts, return the largest subset in which no two parts share more than a chosen length of sequence — on either stnonrepetitive_parts_design — Build a set of new genetic parts that match a degenerate (IUPAC) template and share more than a chosen length with nothing — not each other,Not tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.