About SeqBench
SeqBench is a bioinformatics workbench focused on one thing: making everyday molecular biology computation fast, transparent, and scriptable — for people, and for the AI agents they're starting to work alongside.
Design & simulate
Primer and oligo design, restriction and Gibson cloning simulation, CRISPR guide design, and plasmid annotation — the core loop of a molecular biology workflow, in one place.
Automate
Every tool runs the same calculation whether it's called from the website, a batch FASTA job, a REST API request, or an MCP tool call from an AI agent — including SeqBench-GPT, the conversational design assistant.
Verify
Transparent formulas and documented reference tables — like the NCBI Standard Genetic Code — instead of a black box, so results can be checked against an authoritative source.
Why we built SeqBench
Molecular biology software has traditionally meant a choice between an expensive desktop license and a scattered set of single-purpose web calculators that don't talk to each other. We built SeqBench as a single, stateless workbench that covers the everyday cloning-and-primer-design loop end to end, and exposes every tool the same way — to a browser tab, a script, or an AI agent — instead of locking it behind a UI. For multi-step design in plain language, SeqBench-GPT plans the workflow, runs the tools, and will not mark a construct finished without an independent verification step. We work in bioinformatics ourselves and use these tools for day-to-day sequence design work, which is why development tends to track real lab tasks — cloning, CRISPR guide design, primer and oligo specificity — rather than a long tail of rarely used features.
Data handling
Sequence calculations run server-side through a stateless API, so the same tools power the website, the REST API, and the MCP server. Submitted sequences are processed in memory to compute a result and are not stored or logged. Tools that retrieve public records, such as accession lookup, send only the public identifier needed to complete the request. See the Privacy Policy and Terms of Service for details.
Accuracy & standards
Tools use transparent formulas, reference tables, and documented assumptions where possible, such as the Standard Genetic Code (NCBI table 1) for translation. Results are provided for research and educational use — SeqBench is not intended for clinical or diagnostic use. Please verify critical results against an authoritative source before relying on them.
Get in touch
Questions, bug reports, or feature requests can be sent through the feedback form or to seqbench.bio@gmail.com.