A Free SnapGene & Benchling Alternative in Your Browser
SeqBench is a web workbench for editing plasmids and running everyday molecular-biology analysis, with nothing to install. Its SeqStudio editor opens and exports SnapGene .dna files, remaps features live as you edit, simulates Gibson / Golden Gate / restriction / blunt / TOPO-TA / LIC / SLIC / In-Fusion cloning, plans Gateway BP/LR reactions, searches a whole folder of your constructs at once, reads Sanger .ab1 traces, and is backed by 91 DNA, RNA and protein tools.
It brings editing, cloning design, verification and automation into one focused workspace that is ready whenever you open the browser.
SeqBench vs SnapGene vs Benchling
| Aspect | SeqBench | SnapGene | Benchling |
|---|---|---|---|
| Access model | Web app — nothing to install | Licensed desktop app | Cloud R&D workspace |
| Price | Free | Paid license | Paid (free academic tier) |
| Editable plasmid workbench | Yes — SeqStudio, live feature remapping + undo/redo, and the wrapped linear view exports as one figure rather than one screenful | Yes | Yes |
| DNA, RNA and protein documents | Yes — a document knows which it is, and the panels whose chemistry does not apply are hidden rather than answering: no enzymes or primers on a transcript, no digest on a protein | Yes — separate DNA, RNA and protein file types | Yes |
| SnapGene .dna files | Read & write (import + Export .dna), and the segments this reader cannot model are handed back byte-identical | Native | Import only |
| GenBank import / export | Yes — fuzzy, partial, remote and between-base locations included | Yes | Yes |
| Restriction analysis + virtual gel | Yes — a lane per enzyme (up to six) beside the combined digest, and the partial-digest series that explains bands a complete digest does not predict | Yes | Yes |
| Translation / ORFs / primer design | Yes — 13 NCBI genetic codes, from a CDS's own /transl_table or picked per document; primer design handles a target across the origin, and filters on poly-X, a 3' GC clamp, 3'-end stability and regions no primer may sit on | Yes | Yes |
| Cloning simulation | Gibson, Golden Gate (+ junction fidelity), restriction/ligation including blunt ends, TOPO/TA, LIC, SLIC and In-Fusion/CPEC — plus a Gateway BP/LR planner, which validates the reaction rather than building a product | Yes | Yes |
| Sanger trace (.ab1) viewer | Yes — built-in chromatogram viewer | Yes | Limited |
| Plate-scale clone verdicts | Yes — a facility folder or ZIP of reads in, one verdict per clone out, each citing the positions it rests on | Aligns many reads to one reference in a single view; reading a verdict per clone off it is yours to do | Read alignment |
| Cloning failure diagnosis | Yes — causes ranked by what the design and your controls imply, the ones your evidence eliminates reported as ruled out, and never a probability | No | No |
| Construct history / provenance | Yes — steps logged, and a multi-level ancestry tree that reaches back through each parent's own parents, carried in the file | Yes — parent tree inside the file | Yes |
| Offline access | Installable PWA with offline access to previously opened pages | Yes — native desktop app | No |
| Enzyme library | 566 curated restriction enzymes with supplier, isoschizomer and methylation data, named enzyme sets, and enzymes you define yourself | Yes — enzyme sets | Yes |
| Vector and parts libraries | 617 reusable parts sourced from 308 annotated public vector records, with transparent source coverage | Yes — bundled vector and parts libraries | Yes |
| Search across a folder of files | Yes — locally index a folder of .dna/.gb files in supported browsers, and search by name, feature or exact sequence on both strands and across a circular origin; every hit names the rule that matched it, and files the index could not search are listed with the reason | Yes — Project folder search over file names, sequence and annotation filters | Yes — across what you have uploaded |
| Primer inventory across constructs | Yes — one lab-wide primer list, asked which of your primers bind a template and which pairs amplify it | No lab-wide list — primers live in each file, though a list can be bulk-imported into many files at once | Yes — registry oligos |
| In-workbench AI assistant | Yes — evidence-backed proposals cite the deterministic tool result behind every base and verdict | No | Varies by plan |
| Data handling | Local-first workbench; connected analyses use stateless in-memory processing. The optional assistant previews its context and supports metadata-only mode | On your computer | In the cloud |
Comparison is simplified and provided in good faith — check each vendor for current pricing and features. SnapGene and Benchling are trademarks of their respective owners and are not affiliated with SeqBench.
What SeqBench is great for
- Editing plasmids and opening/exporting SnapGene .dna files in the browser
- Simulating cloning and checking primers straight from the browser
- Reading Sanger .ab1 traces, and picking clones from a whole plate of them
- Searching every construct file in a folder at once, without copying any of them
- Students, core facilities, and labs that want zero-install access
Built for flexible workflows
- Installable PWA with fast access to previously opened pages
- Local-first editing, file handling and folder search
- Reusable vector parts and a lab-wide primer inventory
- Construct ancestry carried with the design
- Evidence-backed AI proposals with user-controlled context
- Batch workflows for plates and multi-sequence projects
The workbench and tools that overlap with SnapGene
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.
Render a circular or linear map with restriction sites.
Find recognition and cut sites for common restriction enzymes.
Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning.
View an .ab1 / .abi Sanger chromatogram, read the base calls and export the trace.
Open a SnapGene .dna file and read its sequence, features, colours and primers — no SnapGene, no account.
Translate a nucleotide sequence to protein in any or all six reading frames.
Find open reading frames in all six frames and translate them.
Estimate primer Tm, GC% and molecular weight from a sequence.
Frequently asked questions
Is SeqBench a free alternative to SnapGene?
Yes. SeqBench's SeqStudio workbench is a free, browser-based editable plasmid and sequence editor that covers the everyday SnapGene workflow: an editable map with live feature remapping and undo/redo, restriction-site scans against 566 curated enzymes with a virtual gel, translation, ORF finding, primer design, and cloning simulation (Gibson, Golden Gate with junction fidelity, restriction/ligation including blunt ends, TOPO/TA, LIC, SLIC and In-Fusion/CPEC, plus Gateway BP/LR planning). It reads and writes SnapGene's .dna format, includes 617 reusable parts sourced from 308 annotated public vector records, and installs as a PWA for fast return access. For most day-to-day cloning and analysis, it is a genuine replacement.
Can SeqBench open and export SnapGene .dna files?
Both, and you do not have to open the editor to do either. The SnapGene Viewer opens a .dna in the browser and shows its sequence, colour-coded features and saved primers, and converts it to GenBank. SeqStudio imports and exports .dna alongside GenBank, so you can open a colleague's file in the browser, edit it, and hand it back in the format their workflow expects. The round trip preserves sequence, topology, feature spans (including spliced and circular-origin features), free-form qualifiers, reading frames, feature colours and the primer library. GenBank fuzzy, partial, remote and between-base locations come back exactly as they arrived, while unmodelled .dna segments are retained byte-identically whenever their coordinates remain valid.
How is SeqBench different from Benchling?
SeqBench focuses on fast sequence design and analysis: editing plasmids, opening and exporting .dna files, simulating cloning, checking primers, reading traces, and screening whole plates of clones. Benchling is organized around cloud R&D operations. Teams can choose the workspace that best matches the task at hand.
Do I have to upload my sequence?
SeqStudio is local-first: editing, annotation, restriction digests, virtual gels, translation, primer design, cloning simulation, plate verdicts, folder search, primer inventory, ancestry and file import/export run in your browser. Connected analyses use transient in-memory processing and do not retain submitted sequences. The optional assistant previews the context it will use and offers metadata-only mode. Full service-specific details are available on the Privacy page.
Can SeqBench search across all my construct files at once?
Yes. In supported browsers, point SeqStudio at the folder where your .dna and .gb files already live and it indexes them in place, then answers questions such as which plasmids contain a sequence, carry a feature, or reuse an insert. Searches cover both strands and circular-origin matches, and every candidate is verified against the real bases before it is shown.
Can SeqBench tell me which clones to grow up, or why a cloning failed?
Both. Plate screening groups a facility folder or ZIP by clone and returns one evidence-linked verdict per clone — PASS, POINT_MUTATION, INDEL, VECTOR_ONLY, WRONG_INSERT, LOW_COVERAGE or AMBIGUOUS. The Cloning Troubleshooter combines the intended design with colonies, controls, gel bands and screening results to rank plausible causes, mark ruled-out explanations, and identify the next observation that best separates the leading candidates.