# SeqBench > Edit plasmids and SnapGene .dna files, design primers, simulate cloning (Gibson, Golden Gate, restriction, LIC and SLIC), find CRISPR guides, and verify sequencing results — all in one browser workbench. ## Workflows - [DNA Sequence Analyzer — Complete Sequence Report](https://seqbench.com/tools/sequence-analyzer): Generate composition, ORF, restriction-site and primer summaries from one sequence. - [Cloning Simulator — Gibson & Golden Gate](https://seqbench.com/tools/cloning-simulator): Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning. - [Batch FASTA Processor: One Tool, Every Sequence](https://seqbench.com/tools/batch-sequence-processor): Apply one operation to every record in a multi-FASTA and export a single CSV/TSV table. - [Batch Workflow — Sequence Pipeline Builder](https://seqbench.com/tools/batch): Chain several tools into a pipeline and run it over every record in a multi-FASTA. - [Construct QC Linter — Check a CDS Before Cloning](https://seqbench.com/tools/construct-qc): Scan a coding sequence for premature stops, cryptic RBS/polyA signals, unwanted restriction sites, GC extremes and repeats. - [Characterize Unknown Sequence](https://seqbench.com/tools/characterize-sequence): Paste any unknown sequence and get a full identity report, then send it to BLAST. - [Batch Editing Quantification — A Whole Plate of Edited Wells Against One Control](https://seqbench.com/tools/editing-plate-quantification): One untreated control against 24-96 edited wells and one sortable table out: indel, base-editing or knock-in percentage per well, each with the fit numbers behind it. - [Golden Gate from Part Plasmids — MoClo Assembly Simulator](https://seqbench.com/tools/golden-gate-from-parts): Digest level-0 part plasmids with a Type IIS enzyme and let the overhangs decide the assembly order. - [Variant to Construct — Mutagenesis and Genotyping Primers from One Variant](https://seqbench.com/tools/variant-to-construct): Turn one variant description into one oligo order table: the primers that build it and the primers that genotype it. - [Verify Assembly — Check an Assembled Plasmid Against Its Parts](https://seqbench.com/tools/verify-assembly): Paste the recipe you ran and the sequence you got. It re-runs the assembly from the parts and diffs the whole molecule against your claim. ## Sequence manipulation - [Reverse Complement Tool for DNA & RNA Sequences](https://seqbench.com/tools/reverse-complement): Calculate the reverse, complement or reverse complement of a DNA/RNA sequence. - [Sequence Formatter & DNA/RNA Converter](https://seqbench.com/tools/format-sequence): Clean, case-convert, wrap, reverse and convert between DNA and RNA. - [Random DNA / RNA / Protein Sequence Generator](https://seqbench.com/tools/random-sequence): Generate random sequences with an optional GC target. - [DNA Motif & Pattern Finder (IUPAC)](https://seqbench.com/tools/motif-finder): Search a sequence for a motif with IUPAC codes, mismatches and both strands. - [Fetch Sequence by Accession (NCBI, UniProt)](https://seqbench.com/tools/sequence-fetcher): Paste a GenBank, RefSeq or UniProt accession and get the FASTA or GenBank record. - [Sequence Format Converter — FASTA ⇄ GenBank ⇄ TSV](https://seqbench.com/tools/sequence-format-converter): Convert between FASTA, GenBank and tab-separated formats, and extract CDS or protein sequences. ## Translation & ORFs - [Translate DNA to Protein (Six-Frame)](https://seqbench.com/tools/translate): Translate a nucleotide sequence to protein in any or all six reading frames. - [Codon Adaptation Index (CAI) Calculator](https://seqbench.com/tools/codon-adaptation-index): Score a coding sequence's codon usage against an expression host, before optimising. - [ORF Finder — Open Reading Frames](https://seqbench.com/tools/orf-finder): Find open reading frames in all six frames and translate them. - [Codon Optimization Tool](https://seqbench.com/tools/codon-optimizer): Optimise a protein or CDS for expression in E. coli, human, yeast, CHO, Pichia and more. - [Reverse Translate Protein to DNA](https://seqbench.com/tools/reverse-translate): Back-translate a protein to DNA using most-frequent or degenerate IUPAC codons. ## Analysis & design - [GC Content Calculator for DNA & RNA](https://seqbench.com/tools/gc-content): Calculate GC%, AT% and per-base composition for DNA or RNA. - [Primer Tm Calculator – Melting Temperature & GC%](https://seqbench.com/tools/primer-tm): Estimate primer Tm, GC% and molecular weight from a sequence. - [Oligo Analyzer – Tm & Dimer Calculator](https://seqbench.com/tools/oligo-analyzer): Nearest-neighbor Tm, ΔG, hairpins and primer dimers for any oligo or primer pair. - [Oligo Cofold — Primer-Dimer & Hairpin ΔG with ViennaRNA](https://seqbench.com/tools/oligo-cofold): Fold one oligo, or two together, with ViennaRNA's loop model at your annealing temperature — hairpin, self-dimer and heterodimer ΔG, plus the interaction ΔG. - [PCR Primer Designer — Design Primer Pairs Online](https://seqbench.com/tools/primer-designer): Design ranked PCR primer pairs from a template, with Tm, GC and dimer checks. - [Site-Directed Mutagenesis Primer Designer](https://seqbench.com/tools/site-directed-mutagenesis): Design SDM primers from a nucleotide or amino-acid change, QuikChange or Q5 style. - [Restriction Enzyme Site Finder](https://seqbench.com/tools/restriction-sites): Find recognition and cut sites for common restriction enzymes. - [Double Digest Buffer Finder - Two Restriction Enzymes, One Tube](https://seqbench.com/tools/double-digest): Pick two restriction enzymes and get the single buffer that runs both, each enzyme's activity in every buffer, and a straight answer on when to digest sequentially instead. - [FASTA / FASTQ Statistics & Validator](https://seqbench.com/tools/fastq-stats): Summarise and validate FASTA or FASTQ: counts, N50, GC, quality. - [DNA & RNA Molarity Calculator (ng ↔ pmol)](https://seqbench.com/tools/dna-molarity): Convert between mass, moles, molarity and copy number for DNA/RNA. - [Ligation Calculator - Insert:Vector Molar Ratio to Microlitres](https://seqbench.com/tools/ligation-calculator): Turn a 3:1 insert-to-vector molar ratio into the microlitres you actually pipette, for one insert or a whole multi-fragment assembly. - [In-silico PCR — Predict Primer Amplicons Online](https://seqbench.com/tools/in-silico-pcr): Enter a template and two primers to predict the PCR product, its size and position. - [CRISPR Guide RNA Designer & PAM Finder](https://seqbench.com/tools/crispr-grna-designer): Scan a sequence for SpCas9, SaCas9 or Cas12a guide candidates with PAMs and scoring. - [CRISPR Off-Target Checker — CFD-Scored Guide Screen](https://seqbench.com/tools/crispr-off-target-check): Screen a guide's protospacer against curated lab reference genomes — SpCas9 hits ranked by CFD, not by mismatch count. - [Gene ID Mapper — Convert IDs & Find Orthologs](https://seqbench.com/tools/gene-id-mapper): Convert gene symbols, Ensembl, Entrez GeneID, RefSeq and UniProt accessions in batch, and find cross-species orthologs. - [Prime Editing Studio — pegRNA Designer (spacer, PBS, RTT, PE3, twinPE)](https://seqbench.com/tools/prime-editing): Design SpCas9 pegRNAs for any substitution, insertion, deletion or small replacement — spacer, PBS sweep, RTT and 3' extension, PE3 nicking guides, plus twinPE dual-pegRNA design for large edits. - [Prime Editing Efficiency Predictor — Rank pegRNAs with PRIDICT2.0](https://seqbench.com/tools/prime-editing-efficiency): Score every PBS/RTT combination for one prime edit with PRIDICT2.0 and rank the pegRNAs — HEK293 and K562 scores, library percentiles, the full pegRNA, and Golden Gate cloning oligos. - [siRNA / shRNA / ASO Designer — Reynolds/Ui-Tei siRNA & 5-10-5 Gapmers](https://seqbench.com/tools/rna-knockdown): Design knockdown reagents against an mRNA — Reynolds/Ui-Tei-scored siRNAs with ready shRNA cassettes, or 5-10-5 ASO gapmers screened for known liabilities. - [KASP / ARMS Allele-Specific Genotyping Primer Designer](https://seqbench.com/tools/kasp-primers): Design KASP/ARMS SNP-genotyping primers — two allele-specific forward primers with FAM/HEX tails and an engineered ARMS secondary mismatch, plus a common reverse primer. - [Gel Electrophoresis Troubleshooter — Symptom Guide](https://seqbench.com/tools/gel-troubleshooter): Diagnose gel problems (no bands, smearing, wrong size, primer-dimer, degradation) with a fully deterministic symptom guide that links to the right SeqBench tools. - [Base Editing Designer — CBE / ABE gRNA & Bystander/Codon Report](https://seqbench.com/tools/base-editing): Find CBE (C→T) or ABE (A→G) base-editing gRNAs that place your target base in the editor's activity window, with bystander flags and amino-acid consequences. - [RNA Secondary Structure Prediction — MFE Fold (Zuker / Turner)](https://seqbench.com/tools/rna-fold): Fold an RNA to its minimum-free-energy secondary structure — dot-bracket, MFE, base-pair list and an exportable arc diagram, without installing ViennaRNA. - [Gene Explorer — Gene Model, Target Dossier & Expression Fingerprint](https://seqbench.com/tools/gene-explorer): Search a gene and get its exon/CDS structure, a druggability/disease/drug/trial/paper dossier, and a GTEx + Human Protein Atlas expression fingerprint — all in one page. - [Functional Enrichment Analysis — GO & Reactome Over-Representation](https://seqbench.com/tools/functional-enrichment): Test a gene list for enriched GO terms and Reactome pathways with hypergeometric p-values and BH-FDR correction. - [PCR Plate Planner — 96-Well Layout, Opentrons Protocol & Echo Picklist Export](https://seqbench.com/tools/pcr-plate-planner): Lay out PCR reactions on a 96-well plate and export a runnable Opentrons protocol or Echo picklist. - [RBS Designer — Translation Initiation Rate Prediction & 5' UTR Design](https://seqbench.com/tools/rbs-designer): Predict the translation initiation rate at every start codon, and design a 5' UTR to hit a target expression level, with OSTIR and ViennaRNA. - [Diagnostic Digest Planner — Pick the Enzyme That Screens Your Clones](https://seqbench.com/tools/diagnostic-digest): Find the restriction digest that tells your intended construct apart from the empty vector, a flipped insert or a mis-assembly — with the bands you would actually be able to read. - [Golden Gate Overhang Fidelity Calculator - Score Your Own Junction Set](https://seqbench.com/tools/golden-gate-fidelity): Score your 4-base Golden Gate / MoClo overhangs against real published T4-ligase ligation counts: the weakest junction, every risky pair, and how your set compares with a published one. - [Plasmid Stability Checker — Find the Repeats Your Construct Can Delete](https://seqbench.com/tools/plasmid-stability): Locate the exact direct repeats that let a construct recombine away the DNA between them, and build the shortened molecule you would actually recover. - [Band Traceback — Find Where an Unexpected PCR Band Came From](https://seqbench.com/tools/band-traceback): Work backwards from the size you measured: which pairs of priming sites on your template could make a product that big, and can their 3' ends actually extend? - [CRISPR Editing Efficiency from Sanger — Indel Spectrum Without NGS](https://seqbench.com/tools/crispr-editing-efficiency): Drop in an unedited control trace and your edited pool's trace and get the indel spectrum, the unedited fraction, and the R² that says whether the decomposition means anything. - [Multiplex PCR Panel Design — Primers That Work in One Tube](https://seqbench.com/tools/multiplex-pcr-panel): Choose one primer pair per target so no two cross-dimerise, every amplicon is separable on the gel, and one annealing temperature serves the whole panel. - [Vector Library — Browse Annotated Plasmid Vectors and Their Parts](https://seqbench.com/tools/vector-library): 308 publicly deposited vectors with their full GenBank feature tables, and 617 parts harvested from them. - [Cloning Troubleshooter — Why the Cloning Failed, Ranked by Evidence](https://seqbench.com/tools/cloning-troubleshooter): No colonies, every clone empty vector, or no PCR band: get the causes your design and your control plates actually implicate, and the cheapest experiment that separates the top two. - [Base Editing Quantification from Sanger — CBE and ABE Efficiency Without NGS](https://seqbench.com/tools/base-editing-quantification): Load an unedited control trace and your edited pool's trace and get per-position C→T or A→G percentages, their z-scores against your own run's background, and the detection limit those numbers sit on. - [HDR Donor Designer — ssODN & dsDNA Repair Templates with Silent PAM Blocking](https://seqbench.com/tools/hdr-donor-designer): Build a knock-in donor with homology arms around a Cas9 cut site, fold in a PAM-blocking mutation, and get primers that genotype the edit. - [Knock-in Quantification from Sanger — HDR and Prime-Edit Rate](https://seqbench.com/tools/knockin-quantification): Put the intended allele itself in the basis: measure what fraction of the pool carries your knock-in, what fraction is still wild type, and what fraction is NHEJ byproduct — from one control trace and one edited trace. - [Oligo Pool Cross-Dimer Screen — Every Pair in One Pass](https://seqbench.com/tools/oligo-pool-screen): Screen a whole oligo pool for cross-dimers between members, each oligo's own hairpin and self-dimer, duplicates and Tm spread. ## Proteins & peptides - [Protein Hydrophobicity Plot](https://seqbench.com/tools/protein-hydrophobicity-plot): Sliding-window hydropathy plot to spot transmembrane and surface regions. - [Protein Molecular Weight Calculator](https://seqbench.com/tools/protein-properties): Compute molecular weight, isoelectric point, extinction coefficient and composition. - [Protease Digestion & Peptide Mass Calculator](https://seqbench.com/tools/protease-digestion): Digest a protein with trypsin, Lys-C, chymotrypsin and more, and get peptide masses. - [Protein Domain & GO Annotation (InterProScan)](https://seqbench.com/tools/protein-domain-annotation): Submit a protein for domain architecture, family and GO-term annotation via EBI InterProScan. - [AlphaFold Structure Viewer — 3D Prediction with Residue Highlighting](https://seqbench.com/tools/alphafold-viewer): Look up a UniProt accession's AlphaFold prediction, view it in 3D with pLDDT confidence coloring, and highlight residue ranges. ## Alignment & visualization - [Multiple Sequence Alignment (MSA) Viewer](https://seqbench.com/tools/multiple-sequence-alignment): Align several DNA or protein sequences and view a colored alignment with a consensus. - [Virtual Gel — Restriction Digest Simulator](https://seqbench.com/tools/virtual-gel): Predict restriction fragments and see the simulated agarose gel with a ladder. - [Sequence Variant Comparator — Find SNPs & Indels](https://seqbench.com/tools/variant-comparator): Align a query to a reference and list substitutions, insertions and deletions with effects. - [Pairwise Sequence Alignment (Global & Local)](https://seqbench.com/tools/pairwise-alignment): Align two sequences with Needleman-Wunsch or Smith-Waterman. - [Plasmid Map & Sequence Viewer](https://seqbench.com/tools/plasmid-viewer): Render a circular or linear map with restriction sites. - [GenBank Map Viewer with Feature Table](https://seqbench.com/tools/genbank-viewer): Paste a GenBank record and see an annotated circular or linear map with a feature table. - [SnapGene .dna File Viewer — Open a .dna in Your Browser](https://seqbench.com/tools/snapgene-viewer): Open a SnapGene .dna file and read its sequence, features, colours and primers — no SnapGene, no account. - [Sanger Trace Viewer — Read .ab1 Chromatograms](https://seqbench.com/tools/sanger-trace-viewer): View an .ab1 / .abi Sanger chromatogram, read the base calls and export the trace. - [Sanger Read vs Reference — Clone Verification](https://seqbench.com/tools/sanger-vs-reference): Align a Sanger read to a reference and get a pass / needs-review verification report. - [Sequencing Read-Back Verification — NGS/Nanopore Consensus vs Reference](https://seqbench.com/tools/sequencing-readback-verify): Align many NGS/Nanopore/Sanger reads to a reference with minimap2, call multi-read consensus variants, and build a corrected consensus sequence. - [Verify a Construct - Did Your Cloning Actually Work?](https://seqbench.com/tools/verify-construct): Paste what you got back and the PCR you say made the insert. It re-derives the insert, finds it in either orientation, and gives you the exact mismatch positions. - [Plasmid Annotator: Detect Features on a Map](https://seqbench.com/tools/plasmid-annotator): Auto-detect promoters, tags, origins and resistance markers in a plasmid, then run a deep scan against pLannotate's full feature databases. - [What Is This Plasmid? - Identify a Backbone and Find Unexplained Regions](https://seqbench.com/tools/identify-plasmid): Paste an unlabelled plasmid and get its closest classic backbone, whether it looks like a chimera of two, and every stretch that neither a known backbone nor a known feature accounts for. - [Volcano Plot — Differential Expression Visualization](https://seqbench.com/tools/volcano-plot): Plot log2 fold-change vs. significance from a DESeq2/edgeR/limma table, with draggable thresholds. - [Clustered Expression Heatmap — Hierarchical Clustering](https://seqbench.com/tools/expression-heatmap): Cluster and visualize a gene x sample expression matrix with row/column dendrograms. - [HGVS Variant Converter — c. ⇄ g. ⇄ p. Coordinate Converter](https://seqbench.com/tools/hgvs-converter): Convert an HGVS c. variant to genomic (g.) coordinates and predict its protein (p.) effect, via a real, live Ensembl exon map. - [Variant Annotator — ClinVar, gnomAD & Predictor Evidence Card](https://seqbench.com/tools/variant-annotator): Look up a variant by rsID, chrom:pos:ref:alt, or HGVS and get its ClinVar significance, gnomAD allele frequencies, and CADD/SIFT/PolyPhen2/REVEL scores in one card. - [SeqStudio — Real Editable Sequence & Plasmid Editor](https://seqbench.com/tools/seqstudio): Type or paste a sequence and edit it directly — every feature remaps live as you insert, delete, or replace bases, with undo/redo and GenBank import/export. - [FASTQ Deep QC Report — FastQC-Style Read Quality Control](https://seqbench.com/tools/fastq-qc): Per-base quality, GC and length distributions, duplication levels, overrepresented sequences and adapter content, each with a warn/fail verdict. - [Sanger Clone Screening — One Verdict per Clone for a Whole Plate](https://seqbench.com/tools/sanger-clone-screening): Drop a plate of Sanger reads against one construct and get one row per clone: which colonies to grow up, and why. - [Plasmid Identifier — Match an Unknown Plasmid to a Known Backbone](https://seqbench.com/tools/plasmid-identifier): Screen an unknown plasmid against 30 curated common backbones and rank the candidates by identity and coverage. ## Guides - [Reverse Complement of DNA, Explained](https://seqbench.com/guides/reverse-complement-explained): Compute a reverse complement by hand in two steps, then apply it to design a reverse PCR primer from a real target sequence. - [How to Calculate GC Content of DNA (Formula)](https://seqbench.com/guides/how-to-calculate-gc-content): Calculate GC content correctly, then see a worked primer example revealing an 8°C gap between two Tm formulas, and which to trust for annealing temp. - [Primer Design Basics: Melting Temperature (Tm) and GC Content](https://seqbench.com/guides/primer-design-and-melting-temperature): A practical guide to designing PCR primers: target length, GC content, melting temperature formulas (Wallace and salt-adjusted), and matching primer pairs. - [Open Reading Frames (ORFs) Explained](https://seqbench.com/guides/reading-frames-and-orfs-explained): Scan all six reading frames for start and stop codons, follow a worked ORF example, and see exactly how an ORF differs from a CDS or gene. - [Codon Optimization: How It Works, When to Use It](https://seqbench.com/guides/codon-optimization-explained): Optimize a gene for E. coli, human, or yeast: see a worked codon-by-codon example, then check the GC, CAI, and repeat trade-offs before ordering. - [Restriction Enzymes and How to Plan a Digest](https://seqbench.com/guides/restriction-enzyme-digest-guide): How restriction enzymes recognise and cut DNA, the difference between sticky and blunt ends, and how to plan a single or double digest for cloning. - [Phred Quality Scores in FASTQ, Explained](https://seqbench.com/guides/understanding-fastq-and-phred-quality): Decode a FASTQ quality string by hand, see why averaging Phred scores overstates accuracy, and learn how N50, L50 and NG50 fit together. - [Protein Molecular Weight and pI Calculator](https://seqbench.com/guides/protein-molecular-weight-and-pi): Calculate protein molecular weight, pI and extinction coefficient from a sequence, and see why two pI tools disagree. - [DNA/RNA ng to pmol Calculator (With Formula)](https://seqbench.com/guides/ng-to-pmol-conversion): Convert ng to pmol for DNA or RNA with the formula, molar-mass shortcuts, and a free calculator using exact sequence composition, not just length. - [How to Find a Motif or Pattern in a DNA Sequence](https://seqbench.com/guides/finding-motifs-in-dna): What sequence motifs are, how IUPAC codes describe degenerate patterns, and how to search a sequence for a motif on both strands with mismatches. - [DNA vs. RNA: Key Differences Explained](https://seqbench.com/guides/dna-vs-rna): Compare DNA and RNA by sugar, base, and strand, then trace a real transcription example showing why T-to-U swaps miss the mechanism. - [IUPAC Nucleotide Ambiguity Codes: Full Table](https://seqbench.com/guides/iupac-nucleotide-codes): All 11 IUPAC nucleotide codes (R, Y, S, W, K, M, B, D, H, V, N) with meanings, complements, and a worked degenerate-primer design example. - [How to Analyze an Unknown DNA Sequence](https://seqbench.com/guides/how-to-analyze-an-unknown-dna-sequence): Characterise an unknown DNA sequence step by step: composition, ORFs, restriction sites and primers — or get all four in one sequence analyzer report. - [Primer Dimers and Hairpins: How to Avoid Them](https://seqbench.com/guides/primer-dimers-hairpins-and-mispriming): Diagnose primer dimers, hairpins and mispriming from gel bands, then apply the ΔG cutoffs (-9 kcal/mol for hairpins, -5 for dimers) that prevent them. - [How to Design a CRISPR Guide RNA (gRNA)](https://seqbench.com/guides/crispr-grna-design-explained): Design CRISPR guide RNAs using PAM rules for SpCas9, SaCas9 and Cas12a, plus position-weighted on-target and off-target scoring. - [How to Design Site-Directed Mutagenesis Primers](https://seqbench.com/guides/site-directed-mutagenesis-primer-design): Design point-mutation, insertion, and deletion primers for QuikChange or Q5-style mutagenesis, with flanking Tm rules and DpnI/KLD cleanup. - [In Silico PCR: Predict Products Before You Order](https://seqbench.com/guides/in-silico-pcr-explained): Simulate PCR against your template to predict product size and flag every off-target binding site before you order primers. - [How to Read a Plasmid Map](https://seqbench.com/guides/how-to-read-a-plasmid-map): Learn to read plasmid maps and the GenBank format (LOCUS, FEATURES, ORIGIN) behind them, plus a step-by-step order for checking a new construct. - [Pairwise vs. Multiple Sequence Alignment](https://seqbench.com/guides/pairwise-vs-multiple-sequence-alignment): Compare global (Needleman-Wunsch) and local (Smith-Waterman) alignment, learn affine gap-open vs. gap-extend scoring, and see when you need MSA instead. - [How to Verify a Clone with Sanger Sequencing](https://seqbench.com/guides/how-to-verify-a-clone-by-sanger-sequencing): Verify a clone by Sanger sequencing: read the chromatogram, trim low-quality ends, and align the trace to its reference sequence. - [Gibson vs Golden Gate vs Restriction Cloning](https://seqbench.com/guides/gibson-assembly-vs-golden-gate-vs-restriction-cloning): Compare restriction, Gibson, and Golden Gate cloning on scar and fragment limits, then simulate the assembly and design junction primers before ordering. - [Reverse Translation: Protein to DNA Sequence](https://seqbench.com/guides/reverse-translation-and-codon-adaptation-index): Back-translate a protein to DNA using most-frequent or degenerate IUPAC codons, then score it with the Codon Adaptation Index. - [Nearest-Neighbor Tm and ΔG Explained](https://seqbench.com/guides/nearest-neighbor-tm-and-delta-g-explained): Calculate oligo Tm and ΔG from nearest-neighbor stacking energies, and use the same math to flag hairpins and 3'-end dimers before a failed PCR. - [How to Predict a Restriction Digest Gel](https://seqbench.com/guides/predicting-a-restriction-digest-gel): Calculate restriction fragment sizes, then simulate the agarose gel with a ladder using Virtual Gel before you pick a percentage or run one. - [Hydrophobicity Plots for Transmembrane Domains](https://seqbench.com/guides/hydrophobicity-plots-and-transmembrane-domains): Score a sequence on the Kyte-Doolittle scale to flag transmembrane helices past the classic +1.6-2.0 cutoff, then compare with Hopp-Woods. - [Why and How to Generate a Random DNA Sequence](https://seqbench.com/guides/why-generate-a-random-dna-sequence): How a random DNA sequence generator works, why setting a GC target matters, and how to use a scrambled sequence safely as a negative control or filler. - [How to Fetch a Sequence by Accession Number](https://seqbench.com/guides/how-to-fetch-a-sequence-by-accession-number): Fetch an exact GenBank, RefSeq or UniProt record by accession number, decode NM_/XP_ prefixes, and pin the version suffix for reproducible results. - [Converting Between FASTA and GenBank Files](https://seqbench.com/guides/converting-between-sequence-file-formats): Convert between FASTA, GenBank and TSV, and pull a CDS or protein straight from GenBank's FEATURES table, complement strand included. - [In Silico Peptide Mass Fingerprinting Guide](https://seqbench.com/guides/protease-digestion-and-peptide-mass-fingerprinting): Predict trypsin, Lys-C and chymotrypsin cut sites and peptide masses, including the K/R-proline exception and missed cleavages for mass spec matching. - [Batch Processing Multiple Sequences at Once](https://seqbench.com/guides/batch-processing-many-sequences-at-once): Run one operation across a multi-FASTA or chain tools into a pipeline, then export a single CSV table per plate, primer batch, or Sanger read set. - [Identify Unknown Sequence: DNA, RNA or Protein](https://seqbench.com/guides/how-to-identify-an-unknown-sequence): Check whether a sequence is DNA, RNA, or protein by its letters, then send it straight to BLAST — one tool does both steps from a single paste. - [Cloning a Gene From Scratch: A Complete Workflow From Sequence to Verified Construct](https://seqbench.com/guides/cloning-workflow-from-sequence-to-verified-construct): A step-by-step molecular cloning checklist covering source sequence, assembly strategy, primer design, in silico assembly, construct QC, and Sanger verification. - [CRISPR Knockout Workflow: gRNA to Verified Edit](https://seqbench.com/guides/crispr-knockout-workflow-grna-to-verified-edit): Rank guide RNAs, design genotyping primers before you edit, screen clones by PCR, and confirm the edit by sequencing in the right order. - [Protein Expression Construct Checklist](https://seqbench.com/guides/protein-sequence-to-expression-ready-construct): Follow a 5-step checklist that catches cryptic ribosome-binding-site errors codon optimizers miss, covering codon usage through construct QC. - [Why Isn't My PCR Working? Troubleshooting Guide](https://seqbench.com/guides/why-isnt-my-pcr-working): Diagnose no product, multiple bands, primer dimers, and smears in the order they usually turn out to be the real cause, with a fix for each. - [Restriction Digest Not Cutting or Wrong Bands](https://seqbench.com/guides/restriction-digest-troubleshooting): Troubleshoot no bands, extra bands, or an odd-sized uncut lane by symptom, covering star activity, partial digestion, and topology mismatches. - [Colony PCR Troubleshooting: No Bands, Wrong Size](https://seqbench.com/guides/colony-pcr-troubleshooting): Diagnose colony PCR by symptom: no product, faint bands, or inconsistent colonies. Learn junction-spanning primer design for unambiguous results. - [Why Is My Codon-Optimized Gene Expressing Poorly? Common Mistakes to Check](https://seqbench.com/guides/why-is-my-codon-optimized-gene-expressing-poorly): Explains why a codon-optimized gene can still express poorly, covering GC extremes, mRNA structure, cryptic motifs, and protein-level solubility limits. - [Wallace vs. Salt-Adjusted vs. Nearest-Neighbor Tm: How Much Do These Formulas Actually Disagree?](https://seqbench.com/guides/primer-tm-formulas-compared): A data-driven comparison of three primer Tm formulas across primer length and GC content, showing exactly how many degrees C they disagree by and why. - [Golden Gate Overhang Fidelity, Scored Against Real Ligation Data: Three Published Sets vs. Two Naive Designs](https://seqbench.com/guides/golden-gate-overhang-fidelity-tested): Real weakest-link fidelity scores for three published Golden Gate/MoClo overhang sets and two naive designs, computed from T4 and BsaI-HFv2 ligation-count data. - [Type IIS Enzymes for Golden Gate and MoClo Assembly: BsaI, BsmBI, BbsI, and SapI Compared](https://seqbench.com/guides/type-iis-enzymes-golden-gate-reference): Verified recognition sites, cut sites, overhang lengths, and reaction temperatures for BsaI, BsmBI, BbsI, and SapI, mapped to MoClo, the plant Golden Gate toolbox, CIDAR MoClo, and GoldenBraid. - [The Anderson Promoter Collection: A Verified Reference Table for BBa_J23100-Series Constitutive Promoters](https://seqbench.com/guides/anderson-promoter-collection-reference): Verified reference table of the 20 Anderson (BBa_J23100-series) constitutive promoters from the iGEM Registry, with sequences cross-checked against an independent mirror and honestly labeled relative-strength confidence. - [Wiring an AI Agent to Real Bioinformatics Tools via MCP](https://seqbench.com/guides/ai-agents-mcp-molecular-cloning): A worked walkthrough of calling SeqBench's MCP server from an AI agent: one JSON-RPC tools/call example and a full Golden Gate domestication chain with gate/provenance data. - [SnapGene vs Benchling vs ApE vs SMS vs SeqBench: A 2026 Cloning Software Comparison](https://seqbench.com/guides/free-molecular-cloning-tools-compared-2026): An axis-by-axis comparison of SnapGene, Benchling, ApE, SMS, and SeqBench for cloning design: pricing, assembly simulation, APIs, and overhang fidelity checking. - [Free Sequence Tools for an iGEM Season: A Phase-by-Phase Checklist](https://seqbench.com/guides/igem-team-free-tools-checklist): A phase-by-phase checklist mapping free sequence tools to iGEM season tasks: primers, Golden Gate overhang fidelity, pre-synthesis QC, colony verification. - [The Trust Problem With AI-Designed DNA Constructs](https://seqbench.com/guides/trust-problem-ai-designed-dna-constructs): Why AI assistants for cloning and CRISPR design tend to report unverified constructs as finished, and why the fix has to live in code, not in a prompt. - [How to Open a .dna File Without SnapGene](https://seqbench.com/guides/how-to-open-a-snapgene-dna-file): A colleague sent you a .dna plasmid file and you don't have SnapGene. What the format actually is, four ways to read it, and how to convert it to GenBank and back. - [No Bands on Your Gel: How to Find Out Why](https://seqbench.com/guides/why-are-there-no-bands-on-my-gel): An empty lane has about six possible causes and they need different fixes. A systematic way to narrow it down, starting with whether the gel or the reaction failed. - [How to Make a Volcano Plot Without R](https://seqbench.com/guides/how-to-make-a-volcano-plot-without-r): What the axes mean, which p-value column to threshold on, and how to get a publication-ready volcano plot from a DESeq2, edgeR or limma table without writing code. - [Converting Gene IDs: Symbols, Ensembl, Entrez, RefSeq and UniProt](https://seqbench.com/guides/converting-gene-ids-symbol-ensembl-entrez-uniprot): Why joining two gene tables loses half your rows: version suffixes, one-to-many mappings, Excel corrupting symbols, and the hub-and-spoke problem behind two-step conversions. - [What Does pLDDT Mean in an AlphaFold Structure?](https://seqbench.com/guides/what-does-plddt-mean): The four confidence bands, what the colours mean, and the crucial thing pLDDT does not tell you — why two confidently predicted domains can still be in the wrong places. - [How to Run FastQC Without Installing Anything](https://seqbench.com/guides/run-fastqc-without-installing): What each FastQC module measures, the exact warn and fail thresholds it uses, and how to get the same report from a browser without a Java runtime. - [Base Editing Windows and Bystander Edits, Explained](https://seqbench.com/guides/base-editing-window-and-bystander-edits): Why a base editor edits more than the base you targeted, where each editor's activity window sits on the protospacer, and how to pick a guide that gets away with it. - [siRNA, shRNA and ASO Design Rules That Actually Matter](https://seqbench.com/guides/sirna-shrna-and-aso-design-rules): The Reynolds and Ui-Tei rules, why the seed region drives off-target silencing, and how to choose between an siRNA, a vector-expressed shRNA and an RNase H gapmer. - [How to Open an .ab1 File (Without Installing Anything)](https://seqbench.com/guides/how-to-open-an-ab1-file): Your sequencing core sent back a .ab1 and nothing on your machine reads it. What the format is, why renaming fails, and which of the usual recommendations are still alive in 2026. - [How to Design a Ribosome Binding Site for E. coli](https://seqbench.com/guides/how-to-design-a-ribosome-binding-site): Why the same RBS part gives different expression in front of different genes, what a translation-initiation-rate model actually computes, and how to pick a 5' UTR — with real numbers. - [How to Check a Whole-Plasmid Sequencing Result](https://seqbench.com/guides/how-to-check-a-whole-plasmid-sequencing-result): Your nanopore whole-plasmid service returned a consensus and a pile of reads. How to tell a real mutation from a basecalling artefact, and why the consensus alone is not the answer. - [How Allele-Specific Primers Actually Discriminate (KASP and ARMS)](https://seqbench.com/guides/how-allele-specific-primers-discriminate): Most 3'-terminal mismatches amplify perfectly well, which is why allele-specific PCR needs a second, engineered mismatch — and why the two primers of one assay rarely need the same one. - [How to Design a pegRNA: PBS, RTT and the PE3 Nick](https://seqbench.com/guides/how-to-design-a-pegrna): A pegRNA is four design decisions stacked on one oligo. What each part does, why the PBS is a melting-temperature target rather than a length, and which candidate to pick. - [From a Primer List to a Runnable 96-Well PCR Plate](https://seqbench.com/guides/from-a-primer-list-to-a-runnable-pcr-plate): Turning a list of reactions into a plate map, an Opentrons protocol and an Echo picklist — what those files really contain, and which numbers in them you must replace. - [How Long Should a Gibson Assembly Overlap Be?](https://seqbench.com/guides/how-long-should-a-gibson-overlap-be): A Gibson primer carries two temperatures that have nothing to do with each other. Which one the overlap length controls, which one it does not, and what a longer overlap actually costs. - [How to Find an Enzyme That Cuts Your Plasmid Exactly Once](https://seqbench.com/guides/how-to-find-a-unique-cutter): Linearising a plasmid needs a single cutter in the right place. Why most unique cutters are useless, why a linear scan of a circular plasmid lies, and how to read the list. ## Reference - [Codon table](https://seqbench.com/codon-table): Standard genetic code table for translating DNA or RNA codons. - [Amino acids chart](https://seqbench.com/amino-acids): One-letter and three-letter amino acid codes with key properties. - [Restriction enzymes](https://seqbench.com/restriction-enzymes): Common restriction enzymes: recognition sites, cut positions, NEB buffer activity, star activity and an interactive double-digest buffer finder. - [IUPAC codes](https://seqbench.com/iupac-codes): Nucleotide ambiguity codes and their complements. - [Sequence file formats](https://seqbench.com/sequence-file-formats): Quick reference for FASTA, FASTQ, GenBank and related formats. - [Phred quality scores](https://seqbench.com/phred-quality-scores): Phred score meaning, error probabilities and ASCII encodings. - [DNA/RNA molecular weight](https://seqbench.com/nucleic-acid-molecular-weight): Average and exact molecular weights for DNA and RNA sequences. - [CRISPR PAM table](https://seqbench.com/crispr-pam-table): PAM sequences for common Cas nucleases and guide design. - [Primer design table](https://seqbench.com/pcr-primer-design-table): PCR primer design rules for length, GC content and Tm. - [Codon usage tables](https://seqbench.com/codon-usage): Per-codon usage frequencies for E. coli, human, yeast, CHO, Pichia, insect, Arabidopsis and zebrafish. - [NCBI alternative genetic codes](https://seqbench.com/genetic-code-tables): Alternative translation tables and codon reassignments beyond the standard code. - [Amino acid pKa & pI](https://seqbench.com/amino-acid-pka): Side-chain and terminal pKa values and how they set the isoelectric point. - [Oligo & DNA/RNA conversions](https://seqbench.com/oligo-conversion): A260 quantification, ng↔pmol, copy number and oligo resuspension. - [PCR cycling conditions](https://seqbench.com/pcr-cycling-conditions): Reference thermal-cycling steps, temperatures, times and cycle numbers. - [CRISPR gRNA design rules](https://seqbench.com/crispr-grna-design-rules): Spacer length, GC, poly-T and seed-region rules for guide RNA design. - [Antibiotic resistance genes](https://seqbench.com/antibiotic-resistance-genes): Selection markers, mechanisms and working concentrations for cloning. - [Genomics file formats](https://seqbench.com/genomics-file-formats): SAM/BAM flags, VCF, BED and GFF/GTF columns and coordinate systems. - [Cloning & expression vectors](https://seqbench.com/cloning-vectors): Reference table of common cloning and protein expression vectors with backbone size, origin of replication, copy number, selection marker, promoter and fusion tags. - [Protein tags](https://seqbench.com/protein-tags): Common affinity, epitope and solubility protein tags with amino acid sequences, mass, purification/detection and protease cleavage. ## Restriction Enzymes Per-enzyme pages under https://seqbench.com/restriction-enzymes/ — recognition site, NEB buffer activity, star activity, methylation sensitivity, and a live site-finder tool, for each of: - [EcoRI](https://seqbench.com/restriction-enzymes/ecori) - [BamHI](https://seqbench.com/restriction-enzymes/bamhi) - [HindIII](https://seqbench.com/restriction-enzymes/hindiii) - [NotI](https://seqbench.com/restriction-enzymes/noti) - [XhoI](https://seqbench.com/restriction-enzymes/xhoi) - [SalI](https://seqbench.com/restriction-enzymes/sali) - [PstI](https://seqbench.com/restriction-enzymes/psti) - [SmaI](https://seqbench.com/restriction-enzymes/smai) - [KpnI](https://seqbench.com/restriction-enzymes/kpni) - [SacI](https://seqbench.com/restriction-enzymes/saci) - [SpeI](https://seqbench.com/restriction-enzymes/spei) - [XbaI](https://seqbench.com/restriction-enzymes/xbai) - [NcoI](https://seqbench.com/restriction-enzymes/ncoi) - [NdeI](https://seqbench.com/restriction-enzymes/ndei) - [NheI](https://seqbench.com/restriction-enzymes/nhei) - [EcoRV](https://seqbench.com/restriction-enzymes/ecorv) - [HpaI](https://seqbench.com/restriction-enzymes/hpai) - [PvuII](https://seqbench.com/restriction-enzymes/pvuii) - [ScaI](https://seqbench.com/restriction-enzymes/scai) - [StuI](https://seqbench.com/restriction-enzymes/stui) - [ApaI](https://seqbench.com/restriction-enzymes/apai) - [BglII](https://seqbench.com/restriction-enzymes/bglii) - [ClaI](https://seqbench.com/restriction-enzymes/clai) - [DraI](https://seqbench.com/restriction-enzymes/drai) - [MluI](https://seqbench.com/restriction-enzymes/mlui) - [NsiI](https://seqbench.com/restriction-enzymes/nsii) - [SphI](https://seqbench.com/restriction-enzymes/sphi) - [AflII](https://seqbench.com/restriction-enzymes/aflii) - [AgeI](https://seqbench.com/restriction-enzymes/agei) - [AscI](https://seqbench.com/restriction-enzymes/asci) - [AvrII](https://seqbench.com/restriction-enzymes/avrii) - [BspEI](https://seqbench.com/restriction-enzymes/bspei) - [BstBI](https://seqbench.com/restriction-enzymes/bstbi) - [FseI](https://seqbench.com/restriction-enzymes/fsei) - [PacI](https://seqbench.com/restriction-enzymes/paci) - [PmeI](https://seqbench.com/restriction-enzymes/pmei) - [SbfI](https://seqbench.com/restriction-enzymes/sbfi) - [SwaI](https://seqbench.com/restriction-enzymes/swai) - [EagI](https://seqbench.com/restriction-enzymes/eagi) - [HaeIII](https://seqbench.com/restriction-enzymes/haeiii) - [AluI](https://seqbench.com/restriction-enzymes/alui) - [TaqI](https://seqbench.com/restriction-enzymes/taqi) - [MspI](https://seqbench.com/restriction-enzymes/mspi) - [MboI](https://seqbench.com/restriction-enzymes/mboi) - [HinfI](https://seqbench.com/restriction-enzymes/hinfi) - [DdeI](https://seqbench.com/restriction-enzymes/ddei) - [ApoI](https://seqbench.com/restriction-enzymes/apoi) - [BstYI](https://seqbench.com/restriction-enzymes/bstyi) - [ScrFI](https://seqbench.com/restriction-enzymes/scrfi) ## Codon Usage by Organism Per-organism pages under https://seqbench.com/codon-usage/ — full codon usage table with a live codon-optimizer tool, for each of: - [E. coli (K-12)](https://seqbench.com/codon-usage/ecoli) - [Human (H. sapiens)](https://seqbench.com/codon-usage/human) - [Yeast (S. cerevisiae)](https://seqbench.com/codon-usage/yeast) - [CHO (C. griseus)](https://seqbench.com/codon-usage/cho) - [Pichia (K. phaffii)](https://seqbench.com/codon-usage/pichia) - [Insect (S. frugiperda / Sf9)](https://seqbench.com/codon-usage/insect) - [Arabidopsis (A. thaliana)](https://seqbench.com/codon-usage/arabidopsis) - [Zebrafish (D. rerio)](https://seqbench.com/codon-usage/zebrafish) ## Compare - [SnapGene & Benchling alternative for sequence analysis](https://seqbench.com/snapgene-alternative/): How SeqBench's online sequence-analysis tools compare to SnapGene and Benchling. ## API & MCP - [MCP server & REST API docs](https://seqbench.com/mcp): Call every SeqBench tool from AI agents or code — an MCP server (https://seqbench.com/api/mcp) and a JSON REST API (https://seqbench.com/api/v1) for stateless sequence-analysis workflows. - REST: `POST https://seqbench.com/api/v1/` with a JSON body; `GET https://seqbench.com/api/v1` lists all tools and their JSON-Schema inputs. - Batch: `POST https://seqbench.com/api/v1/batch` runs one tool over a whole multi-FASTA; `POST https://seqbench.com/api/v1/workflow` runs a multi-tool pipeline over every record. ## More - All tools: https://seqbench.com/tools - Guides: https://seqbench.com/guides - Reference: https://seqbench.com/reference - About: https://seqbench.com/about - Sitemap: https://seqbench.com/sitemap.xml