Orimolecular workbench
Sign inGet started
VOL. 1 · ISSUE 1ORI — OPEN MOLECULAR WORKBENCH2026
Molecular Biology
Open-source · AI-powered

The open
lab bench for
molecular biology

Visualize plasmids with richly annotated maps. Detect features with profile HMMs that catch variants BLAST misses. Simulate cloning workflows with AI assistance — all free, forever.

Open the workbenchGitHub repository →
Next.js 15·Supabase·HMMER3·SeqViz·Open source · MIT
Live annotation · pUC19
Features detected
6
via profile HMM
Database size
2,700+
curated plasmids
Topology
Circular
2686 bp · ColE1 ori

Platform capabilities

Built for researchers who need precision and full access — without a $350/year subscription.

01

Sequence Visualization

Circular and linear plasmid maps with color-coded feature annotations, restriction enzyme digest sites, and primer binding locations.

GenBank · FASTA · .dna
02

Feature Annotation

Profile HMM database built from 200,000+ annotated plasmids. Catches codon-optimized variants and mutants that traditional BLAST misses.

HMMER3 · MMseqs2
03

AI Co-pilot

Describe your cloning goal. Get restriction enzyme strategies, Gibson assembly designs, and primer sequences — algorithmically verified.

Claude API
In active development

The annotation
database

SnapGene's defining advantage is a proprietary BLAST feature library built from years of curation. We're building a better one — open, reproducible, and based on profile HMMs instead of raw sequence alignment.

Every annotated plasmid from major public repositories is processed through a four-stage pipeline: feature extraction → MMseqs2 clustering at 80% identity → MAFFT multiple sequence alignment → HMMER3 profile construction. The result catches codon-optimized variants, truncations, and mutants that BLAST misses at sub-50% identity.

Pipeline
01
Extract features
From all annotated GenBank records
02
Cluster sequences
MMseqs2 at 80–90% identity
03
Build alignments
MAFFT multiple sequence alignment
04
Profile HMMs
HMMER3 · one profile per cluster
Data sources
SnapGene
Curated reference plasmids
2,550
indexed
iGEM Registry
Parts & devices in progress
—
in progress
Addgene
Depositor-annotated, highest quality
200,000+
planned
NCBI RefSeq
Complete plasmid sequences
—
planned