OpenCloning

Import From Anywhere

Your files, NCBI, AddGene, SnapGene, iGEM…

Engineer Anything

Gibson, Golden Gate, Gateway, In vivo assembly…

Automate Everything

Create scripts, notebooks, templates and forms

Share With Anyone

Export cloning workflows in FAIR Open File Format.

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Import from anywhere

From many online repositories and local files.

Access gene sequences from NCBI

Get plasmid sequences from AddGene or SnapGene

Many other repositories supported!

Support for most cloning methods

Primer design for Homologous Recombination, Gibson...

Engineer anything

Supports most cloning methods and has powerful primer design capabilities.

Automate everything

Use scripts, notebook, forms and templates to speed up design

Get started with scripting

Use cloning kit templates

Programmatically load sequences

addgene_source = AddgeneIdSource(id=1, repository_id="52691", repository_name="addgene")
addgene_result = get_from_repository_id_addgene(addgene_source)

locus_source = GenomeCoordinatesSource(
    id=2,
    type="GenomeCoordinatesSource",
    assembly_accession="GCF_000146045.2",
    sequence_accession="NC_001147.6",
    start=432688,
    end=437345,
    strand=-1,
)
locus_result = genome_coordinates(locus_source)

Programmatically design cloning strategies

insert1 = Dseqrecord("GGTCTCAattaAAAAAttaaAGAGACC", name="insert1")
insert2 = Dseqrecord("GGTCTCAttaaCCCCCatatAGAGACC", name="insert2")
insert3 = Dseqrecord("GGTCTCAatatGGGGGccggAGAGACC", name="insert3")

vector = Dseqrecord("TTTTattaAGAGACCTTTTTGGTCTCAccggTTTT", circular=True, name="vector")

products = golden_gate_assembly([insert1, insert2, insert3, vector], [BsaI])

print(products[0].history())

"""
╙── product (Dseqrecord(o39))
    └─╼ RestrictionAndLigationSource
        ├─╼ insert1 (Dseqrecord(-27))
        ├─╼ insert2 (Dseqrecord(-27))
        ├─╼ insert3 (Dseqrecord(-27))
        └─╼ vector (Dseqrecord(o35))
"""

Capture the entire cloning workflow

Data model for AddGene plasmid

{
    "id": 1,
    "type": "AddgeneIdSource",
    "input": [],
    "repository_id": "65109",
    "repository_name": "addgene",
    "sequence_file_url": "https://media.addgene.org/snapgene-media/v1.7.9-0-g88a3305/sequences/110162/c1c98803-c8ba-44a6-95b8-d6a94097e36f/addgene-plasmid-65109-sequence-110162.gbk",
    "addgene_sequence_type": "depositor-full"
  }

Data model for PCR

{
    "id": 4,
    "type": "PCRSource",
    "input": [
      {
        "type": "AssemblyFragment",
        "sequence": 9,
        "left_location": null,
        "right_location": "32..51",
        "reverse_complemented": false
      },
      {
        "type": "AssemblyFragment",
        "sequence": 1,
        "left_location": "1001..1020",
        "right_location": "4053..4072",
        "reverse_complemented": false
      },
      {
        "type": "AssemblyFragment",
        "sequence": 10,
        "left_location": "1..20",
        "right_location": null,
        "reverse_complemented": true
      }
    ],
    "circular": false
  }