seqbench.com

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).

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) plus Wallace and salt-adjusted estimates, with the length-appropriate recommendation and molecular weights.

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).

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.

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.

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 and hidden alternate-frame ORFs that construct_qc flags — without changing the encoded protein (verified).

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

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) or local (Smith-Waterman) pairwise alignment of two sequences with match/mismatch/gap scoring.

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.

Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a).

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/mouse genome search.

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 — SpCas9-family only; Cas12a's staggered cut needs an explicit editStart/editEnd).

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.

Fetch named entries from a session.

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.

Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g.

Resolve a gene/organism name — or a raw NCBI search term — to candidate accessions, instead of guessing one.

Submit a protein sequence to EBI InterProScan for domain architecture, family and GO-term annotation.

Check an InterProScan job submitted via protein_annotate_submit.

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, separate an unmatched region (normal — your own insert) from a POSSIBLE CHIMERA (a region matching a different known backbone than its neighbor), and report per-match %identity/%coverage.

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 region that neither a curated backbone nor a recognized common feature explains.

Annotate a plasmid against pLannotate's open-source feature library — a much larger signature set (GenoLIB parts + Swiss-Prot, cross-referenced against ~195k Addgene-deposited plasmids) than plasmid_annotate's built-in curated list.

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.

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.

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-reacting pairs.

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}) — no account, no expiry.

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).

Search the live web (via Tavily) for information not covered by SeqBench's own tools — recent literature, protocols, vendor/reagent info, general facts.

Submit up to 1000 ids to UniProt's ID mapping service for a single confirmed-safe hop (e.g.

Check a UniProt id-mapping job submitted via id_map_submit.

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.

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.

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, and row-z-scored values for the Clustered Expression Heatmap visualization.

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 background, using the hypergeometric test with Benjamini-Hochberg FDR correction across all tested terms.

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 resolved through the bundled MANE RefSeq<->Ensembl crosswalk), apply 3'-rule normalization to any del/dup/ins, and predict the protein (p.) effect where that is safely computable.

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 with a warn/fail verdict against FastQC's own published thresholds.

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 option reuses), then drops reads below a minimum length.

Look up a UniProt accession in the AlphaFold Protein Structure Database (CC-BY 4.0).

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).

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.

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, Name — the header row reproduced from PyEcho, a real open-source Echo-picklist generator) for the given PCR reactions, at the same well positions export_plate_layout assigns.

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

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 (known drugs and their mechanism/clinical phase, cross-referenced with indications), ClinicalTrials.gov (trials by gene/condition term), and Europe PMC (top cited papers).

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 ~30 C melting temperature, the reverse-transcriptase template (RTT) that encodes the edit, and the full 3' extension, plus PE3 nicking-sgRNA suggestions 40-90 bp away on the opposite strand.

Design a twinPE pegRNA pair (Anzalone et al.

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 (more than one editable base in the window), and — with a CDS reading frame — classifies each edit's amino-acid consequence (silent / missense / nonsense / stop-loss).

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).

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 for RNase H1, phosphorothioate backbone), and screens each for known liabilities (G-quadruplex motifs, CpG immunostimulation, self-complementarity, GC extremes).

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 (FAM for allele A, HEX for allele B), a deliberate internal ARMS secondary mismatch near the 3' end whose strength complements the natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range.

Predict an RNA secondary structure by minimum free energy (MFE) using a Zuker dynamic program with Turner 1999 nearest-neighbor stacking energies (no pseudoknots).

Run one SeqBench tool over many records at once.

Run a multi-tool pipeline over many records.