# 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. ## Linking a user to a tool with their sequence already in it Append `#seq=` and the URL-encoded sequence (raw bases, a FASTA record, or a GenBank record) to a tool URL, e.g. https://seqbench.com/tools/reverse-complement#seq=ATGGCCAAGTAA — the page opens with it in the main input and computes. The fragment is never sent to the server. Up to 20,000 characters. Works on: - https://seqbench.com/tools/reverse-complement#seq=… — Reverse Complement - https://seqbench.com/tools/translate#seq=… — Translate DNA - https://seqbench.com/tools/sequence-analyzer#seq=… — Sequence Analyzer - https://seqbench.com/tools/primer-tm#seq=… — Primer Tm - https://seqbench.com/tools/oligo-analyzer#seq=… — Oligo Analyzer - https://seqbench.com/tools/primer-designer#seq=… — Primer Designer - https://seqbench.com/tools/in-silico-pcr#seq=… — In-silico PCR - https://seqbench.com/tools/restriction-sites#seq=… — Restriction Sites - https://seqbench.com/tools/orf-finder#seq=… — ORF Finder - https://seqbench.com/tools/codon-optimizer#seq=… — Codon Optimizer - https://seqbench.com/tools/codon-adaptation-index#seq=… — Codon Adaptation Index - https://seqbench.com/tools/reverse-translate#seq=… — Reverse Translate - https://seqbench.com/tools/protein-properties#seq=… — Protein Properties - https://seqbench.com/tools/plasmid-viewer#seq=… — Plasmid Viewer - https://seqbench.com/tools/plasmid-annotator#seq=… — Plasmid Annotator - https://seqbench.com/tools/genbank-viewer#seq=… — GenBank Viewer ## Sequence Analysis & Translation - [Batch FASTA Processor — One Tool or a Chained Pipeline](https://seqbench.com/tools/batch-sequence-processor): Apply one operation — or a chain of them — to every record in a multi-FASTA and export a single CSV/TSV table. - [BLAST Search — Identify a Sequence Against GenBank](https://seqbench.com/tools/blast-search): Paste a sequence and find out what it is, against the whole of GenBank, with the program chosen for you. - [Characterize Unknown Sequence](https://seqbench.com/tools/characterize-sequence): Paste any unknown sequence and get a full identity report, then send it to BLAST. - [CpG Island Finder — Gardiner-Garden & Takai-Jones Criteria](https://seqbench.com/tools/cpg-islands): Find CpG islands by either published definition, with the observed/expected CpG ratio reported separately from GC content. - [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. - [GFF3 Viewer and GFF3 to GenBank Converter](https://seqbench.com/tools/gff3-viewer): Read a GFF3 annotation file as a feature table, and turn it plus its FASTA into a GenBank record with an annotated map. - [DNA Motif Finder & Motif Discovery (IUPAC)](https://seqbench.com/tools/motif-finder): Search for a motif you have, or discover one shared by a set of sequences. - [ORF Finder — Open Reading Frames](https://seqbench.com/tools/orf-finder): Find open reading frames in all six frames and translate them. - [Random DNA / RNA / Protein Sequence Generator](https://seqbench.com/tools/random-sequence): Generate random sequences with an optional GC target. - [Reverse Complement Tool for DNA & RNA Sequences](https://seqbench.com/tools/reverse-complement): Get the reverse complement, complement and reverse of a DNA/RNA sequence at once. - [DNA Sequence Analyzer — Complete Sequence Report](https://seqbench.com/tools/sequence-analyzer): Generate composition, ORF, restriction-site and primer summaries from one sequence. - [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 Formatter & DNA/RNA Converter](https://seqbench.com/tools/format-sequence): Clean, case-convert, wrap, reverse and convert between DNA and RNA. - [Translate DNA to Protein (Six-Frame)](https://seqbench.com/tools/translate): Translate a nucleotide sequence to protein in all six reading frames at once. ## Plasmid Maps & Annotation - [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. - [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. - [Plasmid Map & Sequence Viewer](https://seqbench.com/tools/plasmid-viewer): Render a circular or linear map with restriction sites. - [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. - [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, colors and primers — no SnapGene, no account. ## Protein Expression & Codon Optimization - [Codon Adaptation Index (CAI) Calculator](https://seqbench.com/tools/codon-adaptation-index): Score a coding sequence's codon usage against an expression host, before optimizing. - [Codon Optimization Tool](https://seqbench.com/tools/codon-optimizer): Optimize a protein or CDS for expression in E. coli, human, yeast, CHO, Pichia and more. - [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. - [OD600 to Cells/mL Calculator - Cell Density and Back-Dilution](https://seqbench.com/tools/od600-calculator): Turn an OD600 reading into a cell density, a total cell count, and the volumes for a back-dilution. - [Promoter Calculator — Sigma-70 Promoter Strength and Library Design](https://seqbench.com/tools/promoter-calculator): Find every sigma-70 promoter in a region on both strands, with the free-energy terms behind each transcription rate — then build a library of promoters spanning a range. - [RBS Designer — Ribosome Binding Site Calculator & 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. - [Reverse Translate Protein to DNA](https://seqbench.com/tools/reverse-translate): Back-translate a protein to DNA using most-frequent or degenerate IUPAC codons. - [Ribosome Site Accessibility — What Is Base-Pairing Over Your RBS](https://seqbench.com/tools/translation-switch): Find every stretch of a transcript that can pair over the Shine-Dalgarno sequence or the start codon, with the length and melting temperature of each duplex — the mechanism behind every translational switch, and the first thing to check when a construct is silent. - [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, with nothing to install. ## Molecular Cloning & Assembly - [Cloning Simulator — Gibson & Golden Gate](https://seqbench.com/tools/cloning-simulator): Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning. - [DNA & RNA Molarity Calculator (ng ↔ pmol)](https://seqbench.com/tools/dna-molarity): Convert between mass, moles, molarity and copy number for DNA/RNA. - [Double Digest Calculator: Buffer, Activity and Temperature for Two Enzymes](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. - [Gel Band Size Calculator — Read Sizes Off a Gel Photo](https://seqbench.com/tools/gel-band-size): Mark the ladder on your gel photograph, click a band, get its size in bp. - [Golden Gate Overhang Tool - Design a Junction Set or Score Your Own](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. - [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. - [Unknown Plasmid — What Is It and What Do I Plate On?](https://seqbench.com/tools/identify-unknown-plasmid): Which antibiotic, which host, which backbone, and what will bite you later. - [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. - [Non-Repetitive Parts Calculator — Build a Part Toolbox That Cannot Recombine With Itself](https://seqbench.com/tools/nonrepetitive-parts): Find the largest subset of your parts that share no long stretch of sequence, or design new ones that do not — the property that keeps a multi-part assembly stable and synthesisable. - [Operon Designer — Assemble a Polycistron and Find What the Joins Created](https://seqbench.com/tools/operon-designer): Build a multi-gene operon from a promoter, coding sequences and a terminator, then scan the assembled molecule for the internal promoters, ribosome binding sites and terminators that the joins created. - [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. - [Restriction Enzyme Site Finder](https://seqbench.com/tools/restriction-sites): Find recognition and cut sites for common restriction enzymes. - [RPM to RCF (x g) Calculator - Centrifuge Speed Converter](https://seqbench.com/tools/rpm-rcf-calculator): Convert centrifuge speed to relative centrifugal force and back, for any rotor radius. - [Molarity to Mass Calculator - How Much Reagent to Weigh](https://seqbench.com/tools/solution-molarity-calculator): How many grams to weigh out for a target molarity and volume, with the hydrate trap caught. - [Synthesis Complexity Checker — What a Gene Synthesis Vendor's Filter Will Measure](https://seqbench.com/tools/synthesis-complexity): Measure the repeats, GC extremes, GC transitions, homopolymer runs and hairpins that make a fragment hard to synthesise — each against the threshold vendors publish, with no score and no probability. - [Vector Library — Browse Annotated Plasmid Vectors and Their Parts](https://seqbench.com/tools/vector-library): 309 publicly deposited vectors with their full GenBank feature tables, and 617 parts harvested from them. - [Virtual Gel — Restriction Digest Simulator](https://seqbench.com/tools/virtual-gel): Predict restriction fragments and see the simulated agarose gel with a ladder. ## Sanger Sequencing & Clone Verification - [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. - [Sanger Trace Viewer & Clone Verification](https://seqbench.com/tools/sanger-trace-viewer): Inspect chromatograms, compare a read with its reference, or screen a whole plate of clones. - [Check Sequencing Results Against Your Plasmid Map](https://seqbench.com/tools/sequencing-readback-verify): Align your reads to your own annotated reference and get what each difference DOES — silent, missense at a named codon, or a premature STOP that ends the protein — not just where it sits. - [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. - [Whole-Plasmid Sequencing Check — Consensus vs Your Design](https://seqbench.com/tools/whole-plasmid-sequencing-check): Drop the results your sequencing service sent and the map it should be — every sample of the order checked at once. ## PCR & Primer Design - [Barcode Designer — Sequencing Tags That Cannot Be Misread Into Each Other](https://seqbench.com/tools/barcode-design): Design a set of DNA barcodes that are pairwise far enough apart that a read error cannot turn one into another, or check a set you already have for the pair that will collide first. - [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. - [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. - [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-dimerize, every amplicon is separable on the gel, and one annealing temperature serves the whole panel. - [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. - [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. - [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. - [Primer Tm Calculator – Melting Temperature & GC%](https://seqbench.com/tools/primer-tm): Estimate primer Tm, GC% and molecular weight from a sequence. ## Alignment & Variant Analysis - [Dot Plot Tool - Compare Two Sequences and Find Repeats](https://seqbench.com/tools/dot-plot): See repeats, duplications and inversions that a single best alignment hides. - [HGVS Variant Converter — c. ⇄ g. ⇄ p. Coordinate Converter](https://seqbench.com/tools/hgvs-converter): Convert HGVS between c., g. and p.: a c. variant to genomic coordinates and its protein effect, or a genomic position back onto its MANE transcript — via a live Ensembl exon map. - [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. - [Pairwise Sequence Alignment (Global & Local)](https://seqbench.com/tools/pairwise-alignment): Align two sequences with Needleman-Wunsch or Smith-Waterman. - [Phylogenetic Tree Builder & Newick Viewer](https://seqbench.com/tools/phylogenetic-tree): Build a neighbour-joining tree with bootstrap support, or open a Newick file somebody sent you. - [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. - [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. ## Genomics & Expression Analysis - [Clustered Expression Heatmap — Hierarchical Clustering](https://seqbench.com/tools/expression-heatmap): Cluster and visualize a gene x sample expression matrix with row/column dendrograms. - [FASTA / FASTQ Statistics & Validator](https://seqbench.com/tools/fastq-stats): Summarize and validate FASTA or FASTQ: counts, N50, GC, quality. - [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. - [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. - [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. - [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. - [qPCR Delta Delta Ct Calculator - Fold Change with Error](https://seqbench.com/tools/qpcr-ddct-calculator): Ct values in, fold change out - with the propagated standard error, and the right method picked for your amplicon efficiencies. - [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. ## Protein Analysis & Structure - [AlphaFold Structure Viewer — Open PDB & mmCIF Files, View Predictions](https://seqbench.com/tools/alphafold-viewer): Open a .pdb or .cif file — every chain's sequence, missing residues, ligands and pLDDT — or look up a UniProt accession's AlphaFold prediction in 3D. - [Protein Hydrophobicity Plot](https://seqbench.com/tools/protein-hydrophobicity-plot): Sliding-window hydropathy plot to spot transmembrane and surface regions. - [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, Topology & GO Annotation (InterProScan)](https://seqbench.com/tools/protein-domain-annotation): Domains, GO terms, transmembrane helices and signal peptide, via EBI InterProScan. - [Protein Molecular Weight Calculator](https://seqbench.com/tools/protein-properties): Compute molecular weight, isoelectric point, extinction coefficient and composition. ## Mutagenesis & Genome Editing - [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. - [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. - [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. - [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. - [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. - [sgRNA Array Designer — Express Many Guides From One Non-Repetitive Cassette](https://seqbench.com/tools/sgrna-array): Build a multiplexed CRISPR array that expresses up to 27 sgRNAs from one construct and shares no long stretch with itself — the property that stops it recombining away and getting refused by synthesis vendors. - [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. - [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. ## Cloning QC & Troubleshooting - [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? - [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. - [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. - [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. ## 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): What makes a reading frame open, a worked example of picking the ORF that matters, and exactly how an ORF differs from a CDS or a 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 recognize 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 and theoretical pI from a sequence, read the net-charge curve, and see why two pI tools disagree about the same protein. - [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): Characterize 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 colors 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 artifact, 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): Linearizing 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. - [How to Design a Diagnostic Digest for Clone Screening](https://seqbench.com/guides/how-to-design-a-diagnostic-digest): Choose a restriction digest that separates the intended clone from empty vector, reversed inserts and misassemblies, with a worked gel example. - [CRISPR Sanger Analysis: Indels vs. Base Edits vs. Knock-ins](https://seqbench.com/guides/crispr-sanger-analysis-by-edit-type): Choose the right Sanger analysis for a mixed CRISPR pool: shifted indels, base-edit peaks or one intended knock-in, and know when the fit is not evidence. - [Why Multiplex PCR Fails: Primers, Tm & Gel Bands](https://seqbench.com/guides/why-multiplex-pcr-panels-fail): Learn why good primer pairs fail in one tube, how Tm and cross-dimers constrain a panel, and how to space products for an endpoint agarose gel. - [How to Design an HDR Donor: Arms & PAM Blocking](https://seqbench.com/guides/how-to-design-an-hdr-donor): Design an HDR donor around the cut and intended edit, choose ssODN arm length and strand, and add a PAM block without claiming to predict efficiency. - [Why Plasmids Rearrange: Direct-Repeat Deletions](https://seqbench.com/guides/why-plasmids-rearrange-direct-repeats): Learn how exact direct repeats create plasmid deletion substrates, inspect the candidate products, and redesign and screen an unstable construct. - [Insert:Vector Molar Ratio: Why 3:1 Is Not 3× DNA](https://seqbench.com/guides/insert-vector-molar-ratio-explained): Calculate insert mass from vector mass and fragment length, choose a starting molar ratio, and turn the result into pipettable ligation volumes. - [HGVS c., g. and p. Variant Nomenclature Explained](https://seqbench.com/guides/hgvs-c-g-p-variant-nomenclature): Understand HGVS c., g. and p. descriptions, transcript versions, strand changes and the 3′ rule, with a worked TP53 coordinate conversion. - [Read InterProScan Results: Domains & GO](https://seqbench.com/guides/how-to-read-interproscan-results): Interpret InterProScan signature matches, domain coordinates, E-values, integrated InterPro entries and inferred GO terms without overcalling function. - [Interpret GO Enrichment: FDR & Background](https://seqbench.com/guides/how-to-interpret-go-enrichment-analysis): Interpret GO enrichment p-values, BH-adjusted q-values, fold enrichment and gene overlap, and choose the correct background for an ORA result. - [How to Read a Clustered Gene Expression Heatmap](https://seqbench.com/guides/how-to-read-clustered-gene-expression-heatmap): Learn what heatmap colors mean after row z-scoring, how correlation and Euclidean distance differ, and what a dendrogram can—and cannot—show. - [FASTA vs FASTQ: What Actually Differs](https://seqbench.com/guides/fasta-vs-fastq): FASTQ is FASTA plus one number per base. What that number costs you in file size, why the format needs four lines instead of two, and which one your data should be in. - [Protein Concentration from A280](https://seqbench.com/guides/a280-protein-concentration): The extinction coefficient is three counts and three constants. How to get it right, when the reduced and cystine values differ, and the proteins A280 cannot measure at all. - [Six-Frame Translation, and When You Need All Six](https://seqbench.com/guides/six-frame-translation): Three frames forward, three reverse, and a worked example where every forward frame is junk and the protein is on the minus strand. Plus why this is not the same as ORF finding. - [How to Open a GenBank (.gb / .gbk) File](https://seqbench.com/guides/how-to-open-a-genbank-file): A GenBank file is plain text you can read, but the part you want is the FEATURES table — and the canonical pUC19 record has exactly one feature in it. What to do about that. - [Choosing a Buffer for a Double Digest](https://seqbench.com/guides/choosing-a-buffer-for-a-double-digest): Two thirds of enzyme pairs work at full activity in one buffer. This is about the other third — plus the two things that sink a double digest even when the buffer is perfect. - [How to Calculate Delta Delta Ct (ΔΔCt): Worked Example](https://seqbench.com/guides/how-to-calculate-delta-delta-ct): qPCR fold change by the ΔΔCt method, step by step: average the replicates, normalise to a reference gene, read the sign, then correct for primer efficiency. - [How to Convert RPM to × g: Formula and Speed Table](https://seqbench.com/guides/rpm-to-g-conversion): Convert centrifuge RPM to RCF (× g) and back with the formula, why your rotor's radius changes the answer, and a table of common microcentrifuge speeds. - [CpG Island Criteria Explained, With Worked Examples](https://seqbench.com/guides/cpg-island-criteria): How a CpG island is defined, how the observed/expected CpG ratio is calculated, and why a 100% GC sequence can fail the test while an Alu repeat passes. - [How to Make 0.5 M EDTA, 1 M Tris and Other Lab Stocks](https://seqbench.com/guides/how-to-make-stock-solutions): Masses to weigh for 0.5 M EDTA, 1 M Tris, 5 M NaCl, 1 M MgCl2 and 3 M sodium acetate, the pH steps they need, and why the hydrate on the bottle matters. - [How to Read BLAST Results: E-value, Identity and Query Cover](https://seqbench.com/guides/how-to-read-blast-results): What the E-value, bit score, percent identity and query cover in a BLAST hit mean, with three real searches that show how each one misleads on its own. ## 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. - [Hydropathy scales](https://seqbench.com/hydropathy-scales): Kyte-Doolittle, Hopp-Woods and Eisenberg values for all 20 amino acids, with the window sizes and transmembrane threshold each scale is read with. - [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) ## Codons by Amino Acid Per-amino-acid pages under https://seqbench.com/codon-table/ — the codons that encode one residue, in DNA and RNA, with each synonymous codon's usage fraction in eight expression hosts and the preferred codon marked: - [Alanine (Ala, A)](https://seqbench.com/codon-table/alanine): GCT, GCC, GCA, GCG - [Arginine (Arg, R)](https://seqbench.com/codon-table/arginine): CGT, CGC, CGA, CGG, AGA, AGG - [Asparagine (Asn, N)](https://seqbench.com/codon-table/asparagine): AAT, AAC - [Aspartic acid (Asp, D)](https://seqbench.com/codon-table/aspartic-acid): GAT, GAC - [Cysteine (Cys, C)](https://seqbench.com/codon-table/cysteine): TGT, TGC - [Glutamic acid (Glu, E)](https://seqbench.com/codon-table/glutamic-acid): GAA, GAG - [Glutamine (Gln, Q)](https://seqbench.com/codon-table/glutamine): CAA, CAG - [Glycine (Gly, G)](https://seqbench.com/codon-table/glycine): GGT, GGC, GGA, GGG - [Histidine (His, H)](https://seqbench.com/codon-table/histidine): CAT, CAC - [Isoleucine (Ile, I)](https://seqbench.com/codon-table/isoleucine): ATT, ATC, ATA - [Leucine (Leu, L)](https://seqbench.com/codon-table/leucine): TTA, TTG, CTT, CTC, CTA, CTG - [Lysine (Lys, K)](https://seqbench.com/codon-table/lysine): AAA, AAG - [Methionine (Met, M)](https://seqbench.com/codon-table/methionine): ATG - [Phenylalanine (Phe, F)](https://seqbench.com/codon-table/phenylalanine): TTT, TTC - [Proline (Pro, P)](https://seqbench.com/codon-table/proline): CCT, CCC, CCA, CCG - [Serine (Ser, S)](https://seqbench.com/codon-table/serine): TCT, TCC, TCA, TCG, AGT, AGC - [Threonine (Thr, T)](https://seqbench.com/codon-table/threonine): ACT, ACC, ACA, ACG - [Tryptophan (Trp, W)](https://seqbench.com/codon-table/tryptophan): TGG - [Tyrosine (Tyr, Y)](https://seqbench.com/codon-table/tyrosine): TAT, TAC - [Valine (Val, V)](https://seqbench.com/codon-table/valine): GTT, GTC, GTA, GTG - [Stop (Stop, *)](https://seqbench.com/codon-table/stop): TAA, TAG, TGA ## Compare - [SnapGene & Benchling alternative for sequence analysis](https://seqbench.com/snapgene-alternative): How SeqBench's online sequence-analysis tools compare to SnapGene and Benchling. - [ProtParam alternative](https://seqbench.com/protparam-alternative): How SeqBench's protein properties compare to ExPASy ProtParam — molecular weight, pI and the net-charge curve, extinction coefficient, GRAVY, aliphatic and instability indices. - [Multiple Primer Analyzer alternative](https://seqbench.com/multiple-primer-analyzer-alternative): How SeqBench compares to Thermo Fisher's Multiple Primer Analyzer — hairpins, self-dimers and every cross-dimer in a pool of up to 384 oligos, with 3'-end pairings held to a stricter threshold than internal ones. - [Sequence Manipulation Suite alternative](https://seqbench.com/sequence-manipulation-suite-alternative): A modern alternative to the Sequence Manipulation Suite: reverse complement, six-frame translation, ORF finding, restriction analysis, protein properties and pairwise alignment — free and in the browser, like SMS, but reading .ab1, .dna and GenBank files and callable from a REST API or an AI agent. - [SnapGene vs Benchling: which one do you actually need?](https://seqbench.com/snapgene-vs-benchling): Why the two are not the same category — SnapGene is a licensed desktop file editor, Benchling a cloud platform whose sequence editing sits inside a notebook, registry and inventory — compared on cost, where the data lives, offline use and what a rollout takes. SeqBench covers the editor half and explicitly not the notebook half. - [Chromas alternative](https://seqbench.com/chromas-alternative): How SeqBench compares to Technelysium Chromas for reading Sanger chromatograms — .ab1 and .scf open in the browser with no install, and the read can be compared to a reference rather than only viewed. - [OligoAnalyzer alternative](https://seqbench.com/oligoanalyzer-alternative): How SeqBench compares to IDT's OligoAnalyzer, which asks you to sign in or create an account before it will analyse an oligo — SantaLucia nearest-neighbour Tm that responds to your salt, Mg2+ and dNTP concentrations, hairpins and self-dimers drawn as base-paired alignments, hetero-dimers between two oligos, and a 384-oligo plate screened every pair rather than one oligo at a time. - [ORFfinder alternative](https://seqbench.com/orffinder-alternative): How SeqBench compares to NCBI ORFfinder, whose web version is limited to a subrange of up to 50 kb with a Linux-only stand-alone binary as the documented way past it — six-frame ORF finding in the browser with no fixed ceiling, a 250 kb contig in about 35 ms, and any minimum length rather than five fixed choices. - [De Novo DNA alternative](https://seqbench.com/de-novo-dna-alternative): How SeqBench compares to the Salis lab's De Novo DNA suite, whose pricing page lists no free plan — $138 a month for an academic lab, $1.5k a month for a company, and API access only on the top plan of each track. RBS and promoter strength, RBS and promoter libraries, operon assembly, non-repetitive parts, extra-long sgRNA arrays and synthesis screening, free in the browser, plus a REST API and an MCP server at no cost. - [Vector NTI alternative](https://seqbench.com/vector-nti-alternative): What to use now that Vector NTI is withdrawn — Thermo Fisher stopped selling it on 31 December 2019 and all support ended on 31 December 2020. SeqBench does not read the native .ma4 archives; it reads the GenBank the official Vector NTI Data Export Tool writes, including the multi-record files it produces, and replaces the ContigExpress and AlignX projects that the export does not carry, free and in the browser. ## 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