/ Features
Everything a bench scientist opens in a day.
Talindrew covers the ground SnapGene covers — cloning simulation, enzymes, gels, annotation, alignment, plasmid maps — and then keeps going into structure prediction and drug discovery. In a browser tab.
Everything listed below is built and running today. Where a capability doesn't exist yet, it isn't on this page.
01 / Cloning
Every mainstream cloning strategy, simulated end to end.
Eight strategies run against a real digest-and-ligate engine, not a diagram generator. Six of them have a guided wizard with a worked example; the rest run from the node-graph designer. Each design is checked before you commit to it.
- Restriction cloning — enzyme pair, compatible ends, ligated product
- Gibson Assembly — multi-fragment homology with overlap Tm tuning
- Golden Gate — Type IIS, 4-nt fusion sites, scarless assembly
- Gateway — BP and LR recombination at att sites
- TOPO and TA — topoisomerase kits, A-overhang checking
- In-Fusion and NEBuilder HiFi assembly
- Site-directed mutagenesis — QuikChange and NEB Q5 SDM primers
- Pre-flight design check: overhang compatibility, single-cut verification, methylation blocking
- Standalone digest → ligate → transform simulation
- Node-graph designer for multi-step protocols
EGFP head into the pUC19 MCS, cut EcoRI / BamHI and ligated directionally.
pUC19 MCS
2,686 bp · circular
EGFP head
180 bp · linear
One of six worked examples — switch between all of them.
02 / Primers & PCR
Primers designed with the reaction, not after it.
Cloning primers come out of the strategy itself — tails, overhangs and binding regions are derived from the fragments you gave it. PCR runs as a simulation you can inspect.
- Automatic cloning primer design with strategy-specific tails
- Nearest-neighbour Tm, GC content and length per primer
- PCR simulation with product prediction
- Mutagenic primer design for substitutions, insertions and deletions
- Oligo annealing calculator — duplex Tm plus compatible-overhang enzyme lookup
- Built-in M13, T7, T3 and SP6 priming sites detected on any construct
03 / Restriction enzymes
Pick a set, scan, and see what your host will actually cut.
The digest runs over REBASE through eleven predefined enzyme sets, and it accounts for host methylation — the reason a clean-looking digest fails at the bench.
- Eleven enzyme sets: all commercial, non-redundant, NEB, Thermo/Fermentas
- Cutter-type sets: unique cutters, unique dual cutters, 6+ cutters, Type IIS, Golden Gate, nicking
- Dam, Dcm and EcoKI methylation sensitivity applied to the scan
- Per-enzyme detail: recognition site, cut positions, overhang, isoschizomers, compatible ends
- Vendor availability, NEB buffer activity table and incubation temperature
- Silent mutagenesis to add or remove a site without changing the protein
- Cut sites overlaid on the circular and linear maps
Enzyme set
Host methylation
04 / Gel simulation
Run the gel before you pour it.
Migration is modelled from fragment size against gel percentage, voltage and run time, so you can tell in advance whether two bands will actually resolve.
- Configurable gel percentage, voltage, run time and buffer
- Six MW ladders: NEB 1 kb and 100 bp, GeneRuler 1 kb and 100 bp, TrackIt 1 kb Plus, AmpliSize
- Arbitrary multi-lane layouts with per-lane fragment lists
- Digest fragment sizes fed straight in from a restriction scan
- Import and view SnapGene .gel documents
NEB 100 bp
Gibson fragments
Golden Gate parts
05 / Features & annotations
Paste a sequence, get it annotated.
A 60-feature reference library is matched against your sequence on both strands, with fuzzy matching and circular wrap-around, so a raw paste comes back labelled.
- Automatic detection against 60 common features
- Resistance markers, origins, promoters, tags and priming sites
- Exact and mismatch-tolerant matching, both strands, circular-aware
- Colour-coded feature table with search and type filtering
- Bulk select, copy and delete across features
- Import annotations from BED, GFF3 and GTF tracks
06 / Translation & ORFs
Find the reading frame, then read it.
Six-frame ORF detection, whole-sequence translation, and protein-to-DNA reverse translation weighted by the organism you plan to express in.
- ORF finder across all six reading frames, circular-aware
- Whole-sequence and per-frame translation
- Six-frame translation strips on the linear map
- Reverse translation with best-codon or weighted sampling
- Codon optimisation for 10 organisms with CAI scoring
- E. coli, yeast, human, mouse, CHO, Pichia, B. subtilis, Arabidopsis, Drosophila, insect
- Protein property readout for any translated sequence
07 / Alignment & BLAST
Confirm the clone worked.
Align a Sanger read against your design, or send the construct to NCBI without leaving the tab.
- Needleman–Wunsch global alignment
- Smith–Waterman local alignment
- BLOSUM62 for proteins, configurable match/mismatch and gap penalties for DNA
- NCBI BLAST — blastn, blastp, blastx, tblastn, tblastx
- Databases: nt, nr, refseq_rna, refseq_protein, swissprot, pdbnt, pdbaa
- Sanger read versus reference alignment with a mismatch table
08 / Visualization
Circular, linear, and base by base.
The same sequence in three views that stay in sync — an annotated plasmid map, a linear map with translation strips, and the bases themselves with the complement strand.
- Circular plasmid map with annotations, labels and cut sites
- Linear map with feature arrows, primers and six-frame translations
- Base-level viewer with complement strand and position indices
- Zoom, pan and drag-selection across all three views
- Selection carries between views and into the toolbar
- Sanger chromatogram viewer with per-channel toggles and quality bars
- Export any map as SVG, PNG or PDF
pUC19 MCS + EGFP head
2,839 bp, rendered by the same circular viewer the app uses — the light arc is the EGFP insert dropped into the MCS.
09 / Editing & history
Edit the construct, keep the annotations.
Cut, paste and reverse-complement operations shift and truncate the surrounding features rather than silently orphaning them — and every cloning run is recorded as a diagram of how the construct was built.
- Cut, copy, paste, paste reverse-complement and delete over a selection
- Annotations shift, truncate and reverse with the sequence
- Circular-aware operations across the origin
- Per-tab undo and redo with keyboard shortcuts
- Cloning history diagram — sources, reaction and product, drawn as real maps
- Reopen any product from history as a new sequence
10 / Files & workspaces
Open what your lab already has.
Real parsers, including a binary SnapGene .dna reader — not a rename-and-hope importer. Sequences and workspaces persist per user.
- Import GenBank (.gb, .gbk, .genbank), EMBL and ApE (.ape)
- Import FASTA (.fasta, .fa)
- Import SnapGene .dna, including features and primers
- Import SnapGene .gel documents and Staden .scf
- Import Sanger traces: AB1, SCF and ZTR
- Import annotation tracks: BED, GFF3, GTF
- Export GenBank and FASTA; export maps as SVG, PNG, PDF or DOCX
- Workspaces and sequences saved per user, with multi-document tabs
11 / Search
Find it in the sequence, or in the catalog.
Search runs across the sequence itself and across everything annotated on it, with hits highlighted in whichever view you are in.
- Sequence search with hits highlighted on the circular and linear maps
- Enzyme search by name or recognition site, with autocomplete over the catalog
- Feature search by name and type
- Primer search across detected priming sites
- Plasmid library browser and Addgene lookup
12 / Beyond SnapGene
The parts a sequence editor was never going to do.
Structure prediction, docking and an assistant that can read your workspace — the reason this is one tab instead of four.
- FoldRx: fold → pockets → dock → ADMET → FEP → rank, as one pipeline
- ESMFold structure prediction with confidence scoring
- ADMET profiling: Lipinski, PAINS, hERG, Ames, Caco-2
- AI assistant that reads the active sequence and suggests strategies
- CRISPR gRNA finder with on-target scoring and in-sequence off-target checks
- Gene, variant and disease analysis; UCSC genome and GTEx expression
- Vendor hand-off — build an IDT or NEB order link from a selection
- An MCP server, so the whole toolset is callable from your own agents
13 / Platform
Nothing to install.
SnapGene ships a desktop build per operating system. Talindrew runs in the browser, so the version you open is the current one and your sequences are already there.
- Runs in any modern browser — macOS, Windows, Linux
- No install, no licence server, no per-seat desktop build
- Work persists server-side across machines
- Optional Electron desktop shell
- Free to start, no credit card
Start with a worked example.
Every cloning wizard has a Load demo button. You don't need a sequence of your own to see the whole loop.