A Sequence Manipulation Suite Alternative That Reads Your Files
The Sequence Manipulation Suite has done reverse complements, translations, ORF finding and restriction summaries in the browser for twenty years, for free, with no account. SeqBench does the same list — so this page is not going to pretend that cost or privacy is the difference.
The difference is what happens when the sequence is not already plain text in your clipboard. SMS takes pasted text and returns text. SeqBench opens the .ab1 the sequencing facility sent, the .dna a collaborator shared and the GenBank record you downloaded, draws a map you can edit, and exposes every one of those operations as an API call.
SeqBench vs the Sequence Manipulation Suite
| Aspect | SeqBench | Sequence Manipulation Suite |
|---|---|---|
| Price | Free | Free |
| Account required | No | No |
| Where it runs | 26 of the tools run entirely in your browser; the rest run on the server | In your browser — JavaScript, nothing sent anywhere |
| Reverse complement | Yes | Yes |
| Six-frame translation | Yes — one call returns all six frames, +1..+3 and -1..-3 | Yes — a separate Six Frame Translation tool |
| ORF finding | Yes | Yes |
| Restriction site summary | Yes — every site, plus which enzymes cut once and which do not cut at all | Yes — Restriction Summary and Restriction Digest |
| Picking a buffer for two enzymes | Yes — the shared buffer chosen on the worse of the two activities, with the full activity table and a sequential-digest fallback | No — sites and fragments, not reaction conditions |
| Protein properties | One tool returns molecular weight, theoretical pI, GRAVY, extinction coefficient, aliphatic and instability indices and composition together | Yes — as separate Protein Molecular Weight, Isoelectric Point, GRAVY and Protein Stats tools |
| Melting temperature | Nearest-neighbour thermodynamics, with the salt-adjusted and Wallace values alongside for comparison | A basic Tm inside PCR Primer Stats |
| Pairwise alignment | Yes — with percent identity, gap count and the aligned pair | Yes — Pairwise Align DNA, Protein and Codons |
| CpG islands | No — we have no CpG island finder | Yes |
| Opening the files an instrument gave you | Yes — Sanger .ab1 traces, SnapGene .dna and GenBank records are parsed directly | No — plain sequence text in, text out |
| Plasmid map | Yes — an annotated, editable map, and automatic feature annotation | Text figures — Restriction Map and Primer Map as marked-up sequence |
| Scriptable from code | Yes — every tool behind a JSON REST endpoint, plus a batch endpoint for a whole multi-FASTA | No public API |
| Callable by an AI agent | Yes — an MCP server exposing the same tools | No |
Comparison is simplified and provided in good faith — check the Sequence Manipulation Suite for current behaviour. SMS was written by Paul Stothard and is hosted at bioinformatics.org; it is not affiliated with SeqBench.
Where SeqBench is the better fit
- The sequence arrived as a
.ab1,.dnaor GenBank file - You want a plasmid map rather than a marked-up text figure
- You are choosing a buffer, not just listing cut sites
- You want a modern nearest-neighbour Tm
- You want to call the same function from a script or an AI agent
Where SMS still wins
- CpG island finding, which SeqBench does not do at all
- Small format chores — splitting codons, extracting ranges, one-letter to three-letter amino acid codes
- It is open source, so you can run your own copy
- One page per task, with no interface to learn
The same tools, individually
Calculate the reverse, complement or reverse complement of a DNA/RNA sequence.
Translate a nucleotide sequence to protein in any or all six reading frames.
Find open reading frames in all six frames and translate them.
Find recognition and cut sites for common restriction enzymes.
Compute molecular weight, isoelectric point, extinction coefficient and composition.
Align two sequences with Needleman-Wunsch or Smith-Waterman.
Frequently asked questions
Is the Sequence Manipulation Suite still maintained?
It is still online and still works, which for a set of pure-JavaScript sequence utilities is most of what maintenance means — reverse complementing a sequence does not develop new requirements. Treat it as stable rather than abandoned. The reasons to use something else are not that it broke; they are that it cannot open a .ab1 or a .dna file, cannot draw a plasmid map, and cannot be called from a script.
Does SMS send my sequence anywhere?
No — it runs in your browser, which is one of the reasons it has lasted. SeqBench runs 26 of its tools the same way, in the page with no request at all; the rest run on the server because they need a reference genome, a bundled dataset or more compute than a browser tab should be given. Neither tool is the one to worry about if that is your concern.
What does SeqBench have that SMS does not?
Three things that matter in practice. It parses the files your instruments and collaborators actually send — Sanger .ab1 traces, SnapGene .dna and GenBank records — instead of expecting pasted text. It draws an annotated plasmid map you can edit, rather than a marked-up text figure. And every tool is also a JSON REST endpoint and an MCP tool, so a script or an AI agent can call the same function you just clicked.
What does SMS have that SeqBench does not?
A CpG island finder, which we have not built. SMS also carries a long tail of small format utilities — splitting codons, extracting ranges, converting one-letter to three-letter amino acid codes — that have no equivalent here. If your job is one of those, SMS is the shorter path and there is no reason to switch.
Can I get the same Tm that SMS reports?
Not identically, and that is deliberate. SMS's PCR Primer Stats reports a basic Tm; SeqBench's default is nearest-neighbour thermodynamics, which accounts for stacking and salt and is the number a modern primer design assumes. The salt-adjusted and Wallace values are reported alongside it, so if you need to reproduce an older calculation the figure is there — but they will not agree with each other, and the nearest-neighbour one is the one to plan a PCR on.
Is this an open-source replacement?
No. SMS is open source and SeqBench is not; if running your own copy matters, that is a real difference in SMS's favour and no feature list changes it. What SeqBench offers instead is the API — the same functions callable from your own code without hosting anything.