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Hosted DNA/RNA/protein sequence tools for AI agents — primers, oligos, PCR, cloning, CRISPR design, alignment, and batch pipelines.
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This grade is deterministic and reproducible: the same server surface always yields the same grade under a given algorithm version. It is a real automated assessment computed by the MCPGrade engine from what the probe actually observed — not a fabricated or opinion score. It is not a manual human pentest, so it can miss context-specific risks.
Every signal below was measured directly by the automated probe. The grade is derived only from evidence like this — nothing is assumed.
The SeqBench MCP MCP server exposes 96 tools, focused primarily on web and developer capabilities. Its published description reads: "Hosted DNA/RNA/protein sequence tools for AI agents — primers, oligos, PCR, cloning, CRISPR design, alignment, and batch pipelines". It communicates over Streamable HTTP using the 2026-07-28 protocol revision, and does not require authorization to connect. MCPGrade currently rates SeqBench MCP F — a critical issue was found and the server should not be connected as-is. Its most notable findings include "Cross-tool shadowing" and "Cross-tool shadowing". This report is a deterministic, reproducible automated assessment: the same observed surface always yields the same grade under a given algorithm version, and it is refreshed as new scans arrive and free to read — but it is not a substitute for a manual human security review. Always re-check SeqBench MCP's advertised tools, transport security, and authorization posture before connecting an autonomous agent or sharing sensitive context with it.
Add SeqBench MCP to an MCP client using the endpoint below. Review the grade and findings above before granting an autonomous agent access.
MCP endpoint
https://seqbench.com/api/mcpStreamable HTTP transport. This is the MCP endpoint, not a website — paste it into your MCP client server list rather than a browser.
Captured passively during the read-only scan. Click any value to find servers that match it.
The tools this server advertises via tools/list — names, purposes, and the parameters each accepts, exactly as enumerated read-only.
Reverse, complement and reverse complement of a DNA or RNA sequence.
GC content, AT content and per-base composition of a sequence.
Translate a nucleotide sequence to protein (single frame or all six frames; standard code).
Sorted worst-first. Each finding shows its severity, what it means, its OWASP MCP Top-10 mapping, and a recommended fix — the check id links to the exact methodology row that produced it.
tool: reverse_translate
A tool description tries to alter the model’s use of another tool.
Back-translate a protein to DNA (most-frequent codon per organRecommendationDescriptions must describe only their own tool.
tool: primer_specificity
A tool description tries to alter the model’s use of another tool.
— pair it with in_silico_pcr against your own template for that. Each off-taRecommendationDescriptions must describe only their own tool.
tool: oligo_cofold
A tool description tries to alter the model’s use of another tool.
n wants. Unlike oligo_analysis's fast stack-sum screen this is a full loop modRecommendationDescriptions must describe only their own tool.
tool: construct_autofix
A tool description tries to alter the model’s use of another tool.
frame ORFs that construct_qc flags — without changing the encoded protein (vRecommendationDescriptions must describe only their own tool.
tool: ligation_setup
A tool description tries to alter the model’s use of another tool.
RecommendationDescriptions must describe only their own tool.
tool: golden_gate_from_parts
A tool description tries to alter the model’s use of another tool.
. Distinct from cloning_simulate's `goldengate` method, which does the other jobRecommendationDescriptions must describe only their own tool.
tool: assembly_outcomes
A tool description tries to alter the model’s use of another tool.
d the result to diagnostic_digest to pick a screening enzyme. Reports no probabilRecommendationDescriptions must describe only their own tool.
tool: diagnostic_digest
A tool description tries to alter the model’s use of another tool.
ternatives from assembly_outcomes.RecommendationDescriptions must describe only their own tool.
tool: repeat_instability
A tool description tries to alter the model’s use of another tool.
tion product to diagnostic_digest to screen for it.RecommendationDescriptions must describe only their own tool.
tool: band_traceback
A tool description tries to alter the model’s use of another tool.
RecommendationDescriptions must describe only their own tool.
tool: sanger_indel_spectrum
A tool description tries to alter the model’s use of another tool.
RecommendationDescriptions must describe only their own tool.
tool: crispr_offtarget_check
A tool description tries to alter the model’s use of another tool.
is the same way primer_specificity is used: a useful sanity check within the coverRecommendationDescriptions must describe only their own tool.
tool: crispr_hdr_donor
A tool description tries to alter the model’s use of another tool.
esign engine as primer_design.RecommendationDescriptions must describe only their own tool.
tool: session_create
A tool description tries to alter the model’s use of another tool.
hem into every call. Sessions expire after 24 hours.RecommendationDescriptions must describe only their own tool.
tool: session_get
A tool description tries to alter the model’s use of another tool.
session. Prefer session_run for actually USING the values — it keeps raw seRecommendationDescriptions must describe only their own tool.
tool: session_run
A tool description tries to alter the model’s use of another tool.
e, and optionally store selected result fields back into the session by naRecommendationDescriptions must describe only their own tool.
tool: sequence_fetch
A tool description tries to alter the model’s use of another tool.
t upstream. Use sequence_search first if you only know a gene/organism name, noRecommendationDescriptions must describe only their own tool.
tool: sequence_search
A tool description tries to alter the model’s use of another tool.
p to maxResults hits (accession, title, organism); pass the accession youRecommendationDescriptions must describe only their own tool.
tool: protein_annotate_submit
A tool description tries to alter the model’s use of another tool.
s; poll it with protein_annotate_poll.RecommendationDescriptions must describe only their own tool.
tool: protein_annotate_poll
A tool description tries to alter the model’s use of another tool.
b submitted via protein_annotate_submit. Returns {status, ready:false} while still runnRecommendationDescriptions must describe only their own tool.
tool: plasmid_full_report
A tool description tries to alter the model’s use of another tool.
features (from plasmid_annotate), backbone identity / possible chimera (from plRecommendationDescriptions must describe only their own tool.
tool: plasmid_deep_annotate
A tool description tries to alter the model’s use of another tool.
plasmids) than plasmid_annotate's built-in curated list, and it reports partialRecommendationDescriptions must describe only their own tool.
tool: verify_assembly
A tool description tries to alter the model’s use of another tool.
me method/parts cloning_simulate would use (restriction-ligation, Gibson, or GolRecommendationDescriptions must describe only their own tool.
tool: save_permalink
A tool description tries to alter the model’s use of another tool.
result (e.g. a verify_construct or verify_assembly check) rather than re-pastinRecommendationDescriptions must describe only their own tool.
tool: sequencing_readback_verify
A tool description tries to alter the model’s use of another tool.
RecommendationDescriptions must describe only their own tool.
tool: id_map_submit
A tool description tries to alter the model’s use of another tool.
— poll it with id_map_poll.RecommendationDescriptions must describe only their own tool.
tool: id_map_poll
A tool description tries to alter the model’s use of another tool.
b submitted via id_map_submit. Returns {status, ready:false} while still runnRecommendationDescriptions must describe only their own tool.
tool: volcano_plot_data
A tool description tries to alter the model’s use of another tool.
iling the whole batch.RecommendationDescriptions must describe only their own tool.
tool: export_plate_layout
A tool description tries to alter the model’s use of another tool.
plate diagram; export_opentrons_protocol and export_echo_picklist build their downloadabRecommendationDescriptions must describe only their own tool.
tool: export_opentrons_protocol
A tool description tries to alter the model’s use of another tool.
well positions export_plate_layout assigns. Uses real Opentrons labware/pipette APRecommendationDescriptions must describe only their own tool.
tool: export_echo_picklist
A tool description tries to alter the model’s use of another tool.
well positions export_plate_layout assigns. Assumes a 5 uL Echo-scale PCR reactionRecommendationDescriptions must describe only their own tool.
tool: variant_annotate
A tool description tries to alter the model’s use of another tool.
bridged via the hgvs_convert tool). Returns a ClinVar significance summary,RecommendationDescriptions must describe only their own tool.
tool: prime_editing_efficiency
A tool description tries to alter the model’s use of another tool.
RecommendationDescriptions must describe only their own tool.
tool: rbs_design
A tool description tries to alter the model’s use of another tool.
d supply your existing 5' UTR to get a measured baseline and fold-change fRecommendationDescriptions must describe only their own tool.
tool: (server instructions)
A tool description tries to alter the model’s use of another tool.
d of parsing prose. A gate's `notChecked` list is honest about what it doeRecommendationDescriptions must describe only their own tool.
The server accepts tool enumeration (and likely invocation) with no authentication.
RecommendationRequire OAuth 2.1 authorization for any server exposing non-public tools.
Vantaj uptime monitoring via MCP — manage monitors, heartbeats, incidents, and status pages.
Unified gateway to Algeria's TKAWEN ecosystem: commerce, certification, and AI tools.
Provides access to the Cohereon Doctrine AI safety framework with governance components, tiered access, and agent onboarding.
Agentic rails for complex workflows with receipts, fees, and MCP tool access.
Structural TC39 spec lookup for ECMA-262 and ECMA-402 in AI agents, SHA-pinned and offline-first.
Structural TC39 spec lookup for ECMA-262 and ECMA-402 in AI agents, SHA-pinned and offline-first.
Find open reading frames (ATG…stop) across all six frames.
Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.
Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).
Generate a random DNA, RNA or protein sequence, optionally with a target GC content.
Primer/oligo melting temperature: nearest-neighbour (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with the Wallace rule for shorter oligos, a fixed-100 mM-Na+ Schil
Full oligo analysis: nearest-neighbour Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.
Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a
De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.
Nucleic-acid quantity conversions: molar mass, amount (pmol/nmol), molar and mass concentration, and copy number, from mass ± volume and either a length or a sequence.
Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a nucleotide substitution or an amino-acid codon swap.
Screen two oligos for the most stable heterodimer (cross-dimer) between them.
Self-hosted e-PCR-style screen for off-target amplicons predicted by a primer pair against a small set of curated reference genomes (currently: E. coli K-12 MG1655, B. subtilis 168, human mitochondrio
Minimum-free-energy structure and ΔG for one oligo (hairpin) or two oligos together (homo/heterodimer), using ViennaRNA's published loop model at a temperature you choose — DNA parameters (Mathews 200
Find restriction enzyme recognition sites in a DNA sequence.
Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.
Assemble fragments by Gibson/overlap, Golden Gate (Type IIS) or restriction–ligation, returning the product and junction primers.
Auto-detect common cloning features (promoters, tags, origins, resistance markers, MCS, primers) on both strands. Signatures under 20 bp must match exactly; longer ones tolerate up to ~10% mismatches
Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.
Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs a
Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.
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. Handles one insert or several with independent equivalents (
Golden Gate as the reaction runs: digest pre-domesticated part plasmids with a Type IIS enzyme and assemble them in the order their OVERHANGS dictate. The fragment released from each part is the one c
Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two parts swapped, the backbone self-circularised — as full sequen
Pick the restriction digest that tells your intended construct apart from the wrong ones on a screening gel. Digests every candidate, works out which bands would actually resolve at the chosen agarose
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 same terminator or promoter in a multi-gene assembly let the
Explain a band you measured on a gel. Given the template, both primers and the observed size, it enumerates every pair of priming sites — including a single primer priming both strands — that would gi
Quantify CRISPR editing from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto shifted copies of the control. Returns the indel spectrum (how muc
Choose one primer pair per target so the whole panel works in one tube: no cross-dimer between any two of the primers, every amplicon resolvable from every other on the gel you will run, and one annea
Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.
Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale.
In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass.
Codon-optimise a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.
Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.
Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).
Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation.
Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects.
Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). PREDICTED, NOT MEASURED. No held-out skill statistic is claimed. Both
Screen a guide's protospacer for off-target sites (protospacer match + valid PAM, both strands) against a small curated set of common lab reference genomes (see genomesChecked) — NOT a whole human/mou
Build an HDR donor (homology arms flanking an edit) from a target sequence and either an explicit edit window (editStart/editEnd) or a guide's cut site (guideStart/guideEnd/guideStrand/nuclease — SpCa
Parse a GenBank flat file into its locus, definition, features and sequence.
Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.
Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.
Decode a Sanger ABIF (.ab1 / .abi) chromatogram: base calls, per-base quality, the four dye-channel traces and peak locations.
Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.
One-paste 'tell me everything': auto-detects DNA/RNA/protein, then reports composition, ORFs, single-cutter enzymes, end primers or protein properties, plus a BLAST link.
One-click DNA analysis: composition, ORFs, restriction-enzyme scan (single cutters) and end-primer Tm composed into a single report with a copyable text block.
Start a scratch session that holds several named sequences/values (e.g. vector, insert, forward/reverse primer) for use across multiple tool calls via session_run, instead of re-pasting them into ever
Fetch named entries from a session. Prefer session_run for actually USING the values — it keeps raw sequences out of your context. Use this mainly to inspect or debug what a session currently holds.
Add or overwrite named entries in an existing session.
Run any SeqBench tool, resolving selected arguments from a session's named entries instead of pasting them inline, and optionally store selected result fields back into the session by name. This is th
Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g. NM_000546, NP_000537, P04637, ENSG00000141510). Only the accession is sent upstream. Use se
Resolve a gene/organism name — or a raw NCBI search term — to candidate accessions, instead of guessing one. Returns up to maxResults hits (accession, title, organism); pass the accession you want to
Submit a protein sequence to EBI InterProScan for domain architecture, family and GO-term annotation. Returns a jobId immediately — the job itself takes minutes; poll it with protein_annotate_poll.
Check an InterProScan job submitted via protein_annotate_submit. Returns {status, ready:false} while still running; once FINISHED, also returns the parsed domain architecture, per-match details and de
Screen a query plasmid against a small curated set of common backbones (cloning vectors, expression vectors, BACs — see referencesChecked for the exact list) to identify which one(s) it resembles, sep
One combined view of 'what is this plasmid': recognized common features (from plasmid_annotate), backbone identity / possible chimera (from plasmid_identify), and — the two crossed together — any regi
Annotate a plasmid against pLannotate's open-source feature library — a much larger signature set (GenoLIB parts + Swiss-Prot + FPbase + Rfam, cross-referenced against ~195k Addgene-deposited plasmids
Re-derive a construct's insert from the PCR (template + primers) claimed to have produced it, then check — independently of that claim — whether the expected insert actually appears (either orientatio
Deterministic self-check: given the same method/parts cloning_simulate would use (restriction-ligation, Gibson, or Golden Gate — optionally deriving a part by in-silico PCR first), re-derive the expec
Score a candidate set of 4-base Golden Gate/MoClo junction overhangs against real published T4-ligase ligation-count data: per-overhang specificity, the weakest link in the set, and any risky cross-re
Run a registered tool and save its (arguments, result) pair under a short permanent code that anyone with the link can view read-only (/permalink/{code}). Use this to cite or share a specific result (
Align raw Sanger or NGS reads (FASTA or FASTQ) back onto a claimed reference sequence using minimap2, and report per-read mapping identity plus exact variant positions (substitutions/insertions/deleti
Search the live web (via Tavily) for information not covered by SeqBench's own tools — recent literature, protocols, vendor/reagent info, general facts. Returns a short synthesized answer (if availabl
Submit up to 1000 ids to UniProt's ID mapping service for a single confirmed-safe hop (e.g. Gene_Name -> UniProtKB-Swiss-Prot, or UniProtKB_AC-ID -> Ensembl/GeneID/RefSeq_Protein/Gene_Name). Returns a
Check a UniProt id-mapping job submitted via id_map_submit. Returns {status, ready:false} while still running; once FINISHED, also returns the mapped ids (normalized regardless of which target databas
Look up the orthologous (or paralogous) gene for up to 50 gene symbols in a target species, via Ensembl's homology-by-symbol REST endpoint. Symbols with no homology record are reported in `unmapped`,
Validate a differential-expression table (gene, log2 fold-change, p-value/FDR) and compute -log10(p) plus up/down/non-significant counts at conventional default thresholds (|log2FC|>=1, p<=0.05), for
Hierarchically cluster a genes x samples expression matrix (UPGMA/average, complete, or single linkage; Euclidean or correlation distance) and return the row/column leaf order, dendrogram merge trees,
Over-representation analysis: test which GO terms (biological process / molecular function / cellular component) and Reactome pathways are statistically enriched in a query gene list versus a backgrou
Parse an HGVS "c." variant description (by gene symbol, RefSeq NM_, or Ensembl ENST accession), convert it to genomic (g.) coordinates via a real, live-fetched Ensembl exon/CDS map (transcripts resolv
FastQC-style deep quality-control report for a FASTQ file: per-base quality and content, GC and length distributions, sequence duplication levels, overrepresented sequences, and adapter content — each
Trim FASTQ reads: an ungapped sliding-suffix adapter match (against the same named Illumina adapters as the QC report) followed by a BWA-style 3' quality trim (the same algorithm Cutadapt's own -q opt
Look up a UniProt accession in the AlphaFold Protein Structure Database (CC-BY 4.0). Returns confidence, model version and structure file URLs, or {found:false} when no prediction exists for that acce
Assign a set of PCR reactions (name + forward/reverse primer + optional template label) to wells on a 96-well plate, row-major (A1, A2, … A12, then B1, B2, … up to H12). Returns the well-assignment da
Generate a downloadable Opentrons Python Protocol API (v2, OT-2) script that sets up the given PCR reactions on a 96-well PCR plate, at the same well positions export_plate_layout assigns. Uses real O
Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV (columns: Source Plate Name, Source Plate Type, Source Well, Destination Plate Name, Destination Well, Transfer Volume
One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt, genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" / "TP53:c.215C>G", bridged via the
The real exon/UTR/CDS structure of a human gene's canonical transcript, fetched live from Ensembl (the same exon/CDS map the HGVS Converter tool uses) — for rendering an exon diagram.
A gene/drug-target dossier fanned out to five independent sources in one call: Open Targets (function, tractability, top associated diseases), an NCBI/UniProt plain-English function summary, ChEMBL (k
A gene's tissue-expression fingerprint: per-tissue median TPM from GTEx (v8) and subcellular localization / RNA tissue-specificity / protein class from the Human Protein Atlas, in one call.
Design SpCas9 prime-editing pegRNAs for a substitution, insertion, deletion, or small replacement: for each usable NGG PAM it builds the spacer, a primer-binding-site (PBS) length sweep targeting a ~3
Design a twinPE pegRNA pair (Anzalone et al. 2022) for a replacement too large for a single pegRNA's RTT: a left pegRNA nicks the + strand at/before the replacement window and a right pegRNA nicks the
Predict per-pegRNA prime-editing efficiency for one edit with PRIDICT2.0, and return the top-scoring pegRNA designs ranked by it. Takes the target as context, the edit in brackets, then context — ACGT
Design cytosine (CBE, C→T) or adenine (ABE, A→G) base-editing gRNAs for an SpCas9 target: for each NGG gRNA it reports every editable base inside the editor's activity window, flags bystander edits (m
Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus the siDirect seed-duplex Tm off-target flag (≥21.5 °C, computed on
Design antisense-oligonucleotide (ASO) gapmers against an mRNA target: scans candidate sites, builds the antisense oligo in the standard 5-10-5 architecture (chemically-modified wings, central DNA gap
Design KASP/ARMS allele-specific genotyping primers for a SNP: two allele-specific forward primers differing only at the 3' terminal base (one per allele), each with the standard KASP universal tail (
Predict an RNA secondary structure by minimum free energy (MFE) using a Zuker dynamic program with Turner 1999 nearest-neighbor stacking energies (no pseudoknots). Returns the dot-bracket structure, t
Predict the translation initiation rate at each start codon in a bacterial mRNA using OSTIR, the open-source continuation of the Salis lab RBS Calculator, with ViennaRNA free energies. Returns the pre
Design a 5' UTR / ribosome binding site for a given CDS. Generates a spread of Shine-Dalgarno cores and SD-to-start spacings, scores every one with OSTIR in the context of your own CDS (which matters
Run one SeqBench tool over many records at once. `input` is multi-FASTA or one sequence per line; `tool` is any batchable tool name; `args` are shared arguments. Returns a table of per-record results.
Run a multi-tool pipeline over many records. `steps` is an ordered list of { tool, args?, from? }; each step's chained sequence feeds the next by default. `input` is multi-FASTA or one sequence per li