MCP servercom.seqbench/workbench

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

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 wi

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-circulari

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 str

Quantify CBE/ABE base editing from a pair of Sanger traces — an unedited control and the edited pool — without NGS. At each editable position in the activity window the edited trac

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, flag

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

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.

Work out why a cloning experiment failed: no colonies, every clone empty vector, or no PCR band. Takes your design (method, parts, enzymes, primers, host methylation state) plus wh

Rank every observation you have not yet made by how many open causes it settles WHICHEVER WAY IT COMES OUT, then return the smallest set of observations that settles all of them. T

Assemble fragments by Gibson/overlap, Golden Gate (Type IIS), restriction–ligation (sticky or blunt), TOPO/TA, LIC or SLIC (T4-polymerase chew-back) or In-Fusion/CPEC, returning th

Codon Adaptation Index (CAI) and per-codon relative adaptiveness of a CDS against an expression host, with rare-codon and GC3 analysis.

Codon-optimize a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.

Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, crypti

Lint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.

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 statist

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/guideSt

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) — N

Score SpCas9 guides for on-target activity with Rule Set 3 (DeWeirdt et al., Nat Commun 2022) — the current successor to the Doench 2014 and CRISPRscan scores crispr_grna_design re

Screen two oligos for the most stable heterodimer (cross-dimer) between them.

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 a

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.

Recommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.

Quantify a whole plate of edited samples against ONE untreated control trace and return a single sortable table — the plate-scale form of sanger_indel_spectrum, base_edit_quant and

Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV (columns: Source Plate Name, Source Plate Type, Source Well, Destination Plate Name, Destination W

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

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 th

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, den

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 ad

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 C

Find open reading frames (ATG…stop) across all six frames.

Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.

Over-representation analysis: test which GO terms (biological process / molecular function / cellular component) and Reactome pathways are statistically enriched in a query gene li

GC content, AT content and per-base composition of a sequence.

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 functio

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

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 diagr

CHOOSE a set of 4-base Golden Gate/MoClo junction overhangs, rather than scoring one you already have. Maximizes the fidelity of the set's WEAKEST junction against the same publish

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, an

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 ea

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

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

Submit up to 100,000 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_Protei

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 si

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 K

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 indep

Primer/oligo melting temperature: nearest-neighbor (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with the Wallace rule for shorter oligos, a fix

Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.

Center-star multiple sequence alignment of a multi-FASTA input, with consensus and per-column conservation.

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 wil

Full oligo analysis: nearest-neighbor Tm/ΔG/ΔH/ΔS plus hairpin and self-dimer screening with base-pair diagrams and warnings.

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 par

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 for duplicates and Tm spread — and get back

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 repo

Decompose one Sanger trace into fractions over a set of candidate molecules — the intended construct, the empty backbone, a double insert, a flipped part — instead of onto a generi

Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).

Parse a GenBank flat file into its locus, definition, features and sequence.

Decode a Sanger ABIF (.ab1 / .abi) chromatogram: base calls, per-base quality, the four dye-channel traces, peak locations, and the run's own labels (sample name, well, plate, inst

Read a SnapGene .dna file: sequence, topology, every feature with its span, strand, display color and qualifiers (spliced and origin-spanning features kept as such), and the saved

Search a parts list harvested from the annotated features of the vector library — promoters, terminators, RBSs, polyA signals, origins, selection markers, affinity tags, reporters,

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

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 Addgen

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

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(

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

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,

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 ri

De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.

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

In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass. CNBr masses assume terminal Met becomes homoserine lactone; the

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-

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 prote

Sliding-window hydropathy/hydrophobicity profile (ProtScale-style) over a published amino-acid scale.

Protein properties: molecular weight, isoelectric point, GRAVY, extinction coefficient and composition.

Generate a random DNA, RNA or protein sequence, optionally with a target GC content.

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

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 energ

Given the molecules a cloning reaction could have produced and the sequencing primers you could use, work out which primers separate which pairs of candidates — and return the smal

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-ge

Find restriction enzyme recognition sites in a DNA sequence.

Reverse, complement and reverse complement of a DNA or RNA sequence.

Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).

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-

Assemble two or more Sanger reads into a contig WITHOUT a reference sequence — the forward/reverse pair of one insert, or a set of tiling reads. Orientation is worked out from the

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 ind

Measure the rate of a SPECIFIC intended edit from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto three things at once: the

Judge a whole plate of Sanger reads against one construct and return one row per clone: PASS, POINT_MUTATION, INDEL, VECTOR_ONLY (the insert is absent), WRONG_INSERT (the backbone

Align a Sanger ABIF read to a reference and report identity plus every mismatch, insertion and deletion.

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

Statistics for a FASTA or FASTQ file: count, length distribution, N50, GC content and (FASTQ) mean quality.

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 s

Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.

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.

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 ac

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 (substitutio

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-pa

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 sessio

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

Add or overwrite named entries in an existing session.

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 (≥

Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a base substitution, an amino-acid codon swap, or an insertion/deletion/delins. The edit ca

Read a chromatogram for what the basecaller did not report: positions where a second dye is present under the called base (a heterozygote, or a contaminating template), and bases s

Translate a nucleotide sequence to protein (single frame or all six frames; standard code).

One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt (colon- or hyphen-separated), genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_0005

Align a query to a reference and call variants (substitutions, insertions, deletions) in HGVS g. notation, with optional coding effects.

Turn one variant into one buildable plan: verify the reference allele actually sits where the coordinate says, apply the edit, design site-directed mutagenesis primers to install i

Return one vector from the library: its GenBank accession and version, length, topology, organism/definition, complete sequence, and the full annotated feature table (type, label,

Browse a curated library of publicly deposited, feature-annotated cloning and expression vectors — by name, category (E. coli cloning/expression, yeast, mammalian, plant binary, BA

Deterministic self-check: given the same method/parts cloning_simulate would use (restriction-ligation, Gibson, Golden Gate, LIC, SLIC or In-Fusion/CPEC — optionally deriving a par

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 appear

Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.

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

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

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