com.seqbench/workbench

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 — see genomesChecked for the exact list). This checks background/host-genome specificity, NOT whether the primers hit your intended target — pair it with in_silico_pcr against your own template for that. Batchable over candidate REVERSE primers against one fixed forward primer (screen many candidates against a shared partner) — not independent primer-pair batching, which this tool doesn't support.

In-silico protease/chemical digestion: cleave a protein and report each peptide's position, length and neutral mass.

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 deduplicated GO terms.

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.

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.

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-bracket structure, the estimated MFE (kcal/mol), and the list of base pairs. A from-scratch, in-browser implementation (there is no usable browser ViennaRNA); the simplified loop energy model makes the MFE a good comparative estimate, not a lab-grade absolute.

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 a specific result (e.g. a verify_construct or verify_assembly check) rather than re-pasting it.

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 sent upstream. Use sequence_search first if you only know a gene/organism name, not an accession. For an Ensembl transcript ID this returns spliced cDNA; for a gene ID it returns the full genomic locus (introns included) — Ensembl's own default for each ID type.

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 accession you want to sequence_fetch.

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/deletions), with a consensus view across reads and a corrected consensus sequence (the reference with every consensus-supported edit applied). Complements verify_construct/verify_assembly: those re-derive what a design SHOULD produce from its own stated inputs; this checks what a real sequencer actually read back.

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 every call. Sessions expire after 24 hours.

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.

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 the main way to chain a multi-part design (vector + insert + primers) across calls without shuttling raw sequences through your own context.

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 a siDirect-style seed-duplex Tm off-target flag (≥21.5 °C). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs) and, per candidate, a ready shRNA cassette (sense–loop–antisense–Pol III terminator). Heuristic sequence rules only — no RNA-folding accessibility model and no transcriptome-wide off-target search.

Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a nucleotide substitution or an amino-acid codon swap.

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, genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" / "TP53:c.215C>G", bridged via the hgvs_convert tool). Returns a ClinVar significance summary, gnomAD exome/genome allele frequencies, and CADD/SIFT/PolyPhen2/REVEL pathogenicity predictor scores — each section explicitly null when that source has no data, never silently omitted. See the result's own "caveats" for real data-freshness limits (frozen gnomAD/CADD snapshots, periodic ClinVar snapshot).

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

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 expected WHOLE product and diff it against a claimed final sequence. Returns pass/fail plus the exact position and nature of any discrepancy — not an opinion, the same deterministic simulation SeqBench already runs, run a second time as a check. See verify_construct for a narrower, insert-only check that doesn't require declaring the vector/enzymes/method.

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 orientation) in the claimed final construct, at what identity, and with exact mismatch positions if not. Optionally also checks for a premature stop in a declared reading frame. This re-derives from the claim's own stated inputs; it does not review the claim's prose.

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|>=1, p<=0.05), for the Volcano Plot visualization. Invalid rows (non-finite log2FC, or p-value outside (0,1]) are dropped and reported rather than failing the whole batch.

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 available) plus ranked source snippets with URLs. This does not run any bioinformatics calculation itself; use the dedicated tools for that.

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 line.