SeqBench - Sequence workbench for cloning, CRISPR & primer design, with an AI copilot

SeqBench is a sequence workbench for molecular and synthetic biology that covers the cloning and primer-design loop end to end. Its AI copilot, SeqBench-GPT, searches the literature, plans multi-step designs, and drives real tool calls across primers, cloning, and CRISPR, verifying every construct before reporting it done rather than hallucinating sequences.

What it does: design PCR primers with melting-temperature (Tm) calculations, run in-silico PCR and primer-specificity screening; simulate molecular cloning with Gibson Assembly, Golden Gate Assembly, and restriction digest, with automated construct QC/autofix, a plasmid viewer, and a virtual gel; design CRISPR guide RNAs (gRNA) for gene knockouts; and run sequence analysis including reverse complement, translation, ORF finding, restriction-site mapping, motif search, GC content, codon optimization, multiple sequence alignment, and Sanger verification.

How it works: every tool runs server-side and returns a typed pass/fail gate plus provenance. Batch-process whole plates of FASTA/FASTQ sequences at once, or chain tools into multi-step workflows.

API and integrations: every tool is exposed via a REST API and a Model Context Protocol (MCP) server for AI agents, with a public OpenAPI 3.1 specification, so pipelines and agents can call the same calculations programmatically.

Use cases: molecular cloning, plasmid construction, CRISPR knockout design, primer and PCR design, and automated sequence-analysis pipelines for molecular biology and synthetic biology labs.